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I just had Famitracker freeze (stuttering audio buffer) after loading a file while playing another.
Then I tried it again several times, and it didn't crash.
As for which code is actually getting executed, it varies...
On one trace, I saw this loop:
(lead spaces indicate function calls, decrease of indent indicates returning from a function call)
00431F45
_0043116A
__004694A0
__00477028
_0043117A
00431F83
_00468AA0
00431F8C
_00457651
_0045763A
__GDI32.SetBkColor
__GDI32.ExtTextOutA
0043200E
jumps back to 00431F45
Of course, these hex addresses are nearly useless without debug information (labels), but those GDI32 calls might help to identify which function it's executing.
The actual EXE is the publicly available build I already mentioned above.
I can also see that it calls PeekMessageA a lot.
Oh well, I can't produce anything worthwhile here. Maybe I need to run a debug build.
Actually this might be helpful, because I got something similar and tried to fix it some months ago. I don't remember the details but I think these API calls was close to the bug, so hopefully that won't appear any more.
PeekMessage is called in the sound generator loop.