In my primary project, I recently did a major refactoring which mostly involved shuffling a bunch of files around, but in there was also an update of the ASF code from 3.30 to 3.34.1. For reasons which are too complex to get into, I didn't notice until recently that something in that shuffling of files caused TC3 (and possibly TCC0, performing a different function) to stop triggering its callback every ~60 seconds. The maddening thing is that the enabling code where I configure TC3 is exactly the same, and I've verified (using the debugger) that it IS actually being called (for setting up TC3) in both cases. _Something_ else I've done has clearly had an unfortunate side effect, but I'm having a heckuva time spotting it - best guess is I'm changing something else somewhere later in the code which breaks it. I _also_ have a problem with PWM output which is controlled by TCC0 - prior to the reorg, it worked, but now the LED which is supposed to be PWM-controlled is arbitrarily just on or off, not changing, which leads me to believe TCC0 isn't working either.
Things I've checked: clocks are still set up the same (conf_clocks.h hasn't changed and is definitely being compiled in - if I insert a compilation error, it breaks the compile as expected), the TC enabling code is called. It seems to be that the callbacks are just not getting called. Looking for creative troubleshooting suggestions at this point because I'm a little baffled. :)
If it matters, I see this on a few different boards (supporting different boards was part of the refactor), but I can duplicate both the working and non-working state on a SAMW25 Xplained Pro (SAMD21G18A core).