Since the bug happens on high-frequency interrupts it should happen on the DSP early as the playback uses a 22kHz or 44kHz interrupt, right?
But I think even though the ISA is quiet equal, the DSP is different in so many parts, that it is likely the bug is only in the GPU.
If you just think of the bus width, memory size etc. . So I doubt they used the same RTL for both chips.
I've been following this thread.
I checked my code and I am doing what you were, not what DOOM is.
I have two interrupts turned on in the GPU, one from the OP, the other from the Blitter.
The OP interrupts once per vblank, the blitter interrupts ~10,000 times in a vblank.
So maybe it isn't a frequency problem as much as it is which interrupts are being used.
I've never used the timer interrupt with the GPU.
You said you were doing 1ms timer interrupts. (1000 times a second)
The Blitter is interrupting in the 60k to 80k times a second, and I've never seen this bug.