ROME – At first blush, Aung San Suu Kyi seems a natural Pope Francis favorite. She represents a small and isolated southeast Asian nation, appealing to the pope of the peripheries. She’s a woman in a position of power, and she’s spent her career, much of it under house arrest, battling for human rights and democracy against military rule.

The two met in October 2013, when Suu Kyi was finally able to pick up an honorary citizenship of Rome she’d been awarded in 1994, after which a Vatican spokesman described “a great feeling of harmony and accord” between Francis and his Burmese guest. Two years later, Francis named the first-ever cardinal from Myanmar, Charles Bo, in a clear sign of respect and affection for the country.

Moreover, relations between the Vatican and Myanmar are warming, with the country’s parliament having approved a measure in March to make Myanmar the 183rd nation to enjoy diplomatic relations with the Holy See.

So why did the second meeting of these two global icons on Thursday, as opposed to the first, feel as much like a collision as a love-fest?

Suu Kyi is in Rome to participate in a conference Thursday afternoon organized by the Italian parliament on gender equality and sustainable development, and also met on Wednesday with Italian Foreign Minister Angelino Alfano, who praised her “personal, peaceful commitment to the cause of democracy and human rights.” Also on Thursday, she was to meet Italian Prime Minister Paolo Gentiloni.

The highlight of her schedule, however, was the tête-à-tête with Francis.

There were the usual pleasantries surrounding the encounter, as both figures were smiling and apparently relaxed. Francis presented her with a medallion depicting a desert blooming, illustrating a passage from the Old Testament book of Isaiah, but also a sign of hope for the country.

Yet although no one quite said so out loud, there’s every reason to believe that when Francis and Suu Kyi were behind closed doors, they did more than make nice.

The reason is that while Pope Francis does indeed love an underdog, in the context of Myanmar these days, that’s no longer Suu Kyi, who now serves as State Counsellor, the de facto head of government, but rather an oppressed group of Muslims in the country’s western Rakhine state known as the Rohingya, whose plight has become a special focus of Francis’s concern.

Tens of thousands of Rohingya, perhaps as many as 100,000, are believed to have fled Myanmar, most crossing by land into Bangladesh but others taking boats in an effort to reach Indonesia, Malaysia, and Thailand. In general, those countries don’t feel capable of handling an influx of refugees, and their reception often has been harsh.

Yet the Rohingya continue to flee, escaping what a UN report in February described as a possible “genocide” and set of “crimes against humanity” in Myanmar, where the Rohingya are officially categorized as Bengali “interlopers” despite the fact they’ve lived in Rakhine for generations. They’re subject to systematic discrimination and violence, what the UN also called a “campaign of terror,” and enjoy no citizenship rights – in effect, they’re stateless.

Pope Francis first spoke out on the fate of the Rohingya in August 2015, during a session with youth in Rome.

“Let’s think of those brothers of ours of the Rohingya,” he said. “They were chased from one country and from another and from another. When they arrived at a port or a beach, they gave them a bit of water or a bit to eat and were then chased out to the sea.

“This is a conflict that has not resolved, and this is war, this is called violence, this is called killing!” he said.

One month later, he brought the Rohingya up again in an interview with Portuguese radio.

“Further away from Europe there is another phenomenon which hurt me deeply: the Rohingya, who are expelled from their country, get into boats and leave,” he said.

“They reach a port or a beach, and they are fed and given water and then sent out to sea again, and not taken in. There is a lack of capacity for welcoming humanity.”

Francis came at the subject again in February, saying on the Church’s International Day of Prayer and Awareness against Human Trafficking that “they have been suffering, they are being tortured and killed, simply because they uphold their Muslim faith.

“I would like to pray today with you in a special way for our brothers and sisters Rohingya,” the pontiff said.

“They are driven out of Myanmar, going from one place to another because they’re not wanted. They’re good people, peaceful! They aren’t Christians, they’re good [people]. They’re brothers and sisters of ours,” he said.

The remarks were spontaneous, suggesting the issue is close to Francis’s heart.

For his part, Bo has been equally outspoken, defining the persecution of the Rohingyas as “an appalling scar on the conscience of my country.” He has described them as “among the most marginalized, dehumanized and persecuted people in the world. They are treated worse than animals.”

Addressing the UK parliament in London in May 25, 2016, Bo said no human being deserves to be treated the way the Rohingyas are.

“Without [a solution], the prospects for genuine peace and true freedom for my country will be denied, for no one can sleep easy at night knowing how one particular group of people are dying simply due to their race and religion.”

Bo’s line, and that of the tiny Catholic community in Myanmar (less than one percent of the population of 55 million), stands in stark contrast to hardline elements of the majority Buddhist tradition. Buddhist monks often join protest rallies at ports in Myanmar, for instance, objecting to efforts to deliver humanitarian aid to the Rohingya.

To date, Suu Kyi has either maintained silence or defended the status quo. She recently ruled out Myanmar cooperating with a UN Human Rights Council resolution calling for an investigation, saying it’s not “in keeping with what is actually happening on the ground.”

She’s also denied that ethnic cleansing is taking place, saying “it’s a matter of different sides of the divide, and this divide we are trying to close up.”

Granted, many observers believe Suu Kyi has to walk a fine line given the massive influence the military still wields in Myanmar. Nevertheless, some of the shine seems to have come off her reputation, as several human rights campaigners who used to spend their time campaigning for her release are now attacking her record.

As appalling as the situation with the Rohingya is, it’s not the only issue on which Francis may have had some challenging things to say.

Earlier this year, Myanmar’s military confirmed they had arrested two Protestant clergy and charged them with aiding rebels in the eastern Shan State, after long denying they were in custody. The two were accused of serving as “informers and spreading false news on behalf of the armed insurgents.”

By “spreading false news,” what a military spokesman meant is that the two clergymen had helped journalists cover the military’s bombing of a Catholic church and school in Shan State in late November 2016.

In recent years, organizations of Buddhist radical monks, such as one called “Ma Ba Tha,” have increased their campaigns against religious minorities and successfully helped introduce four laws for the “Protection of Race and Religion,” building almost insurmountable hurdles to conversions and religiously mixed marriages.

Christians in Myanmar often suffer a double whammy. First, because they tend to be concentrated among ethnic minorities, especially the Kachin, they’re targeted for racial reasons. Second, because Christians are often (mis)identified with the West, they’re also seen by radical Buddhist groups as the cultural and political “other.”

The United States Commission on International Religious Freedom recently issued a report on Christian persecution in Myanmar, concluding that Christians face discrimination in employment, forced conversions, violence and desecration of churches and Christian communities.

“Senior leaders in Burma’s government need to publicly acknowledge and remedy the fact that the elevation of Buddhism as the de facto state religion and resulting policies and practices have violated the rights of Christians and other religious and ethnic minorities,” the report concluded.

More than 60 Christian churches have been destroyed in Myanmar’s Kachin state, where the country’s Christian population is concentrated, since a long-standing cease-fire broke down in 2011, according to the British-based Christian Solidarity Worldwide.

For now, we don’t know exactly what cards Francis may have put on the table during his encounter with Suu Kyi. During a news conference on his return flight from Egypt to Rome on April 28, Francis insisted that when he meets a political leader, what transpires stays between them.

“Generally, when I meet with a head of state for a private conversation, it remains private,” he said.

Yet despite that reserve, given the context of what’s happening in Myanmar these days, it’s not difficult to imagine that whatever went on Thursday, it wasn’t entirely sweetness and light.