I bought an Arduino M0 Pro from RS recently, but as well as coming in an "Arduino.org" box, it seems that it's pretty much unsupported here - and the Arduino.org site is gone. PWM doesn't work with the M0 Pro bootloader, only with the Zero one. And then two of the pins are swapped. I've only just started playing with it, so may well discover more issues.
Also - I fully appreciate the .cc/.org kerfuffle, but since that's now resolved why isn't there a forum for the M0 Pro?
Because it SHOULD be the same as the Zero, except for the pinswap (and THAT should be handled transparently, and only bother people who use "direct port IO")
PWM doesn't work with the M0 Pro bootloader
This is the first that I've heard that PWM has problems on the M0 Pro. Even if true, that should have nothing to do with the bootloader! Could you provide the usual "I think I found a bug" details, like your code, which pins, which version of the IDE and core you're using, and so on? The SAMD processors have two kinds of timers, and there are some differences between the variant.cpp files WRT Timers/PWM that I don't understand, so this COULD be a real bug caused by "version skew."