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Thanks Koitsu. I am very familiar with rdanbrook but figured id post this here since it seems this community is really awesome when it comes to helping others er noobs like me hahah.

I know this isn't a nestopia forum but figured id see what everyone who has more knowledge than I could say as to what the issue might could be. Quite frankly, I am astounded this was never noticed until now. Its been around a VERY long time in nestopia, I tested versions going back to 1.20 or something and the bug is still there.

MMC5 is still to this day one of the less-understood mappers (compared to others). Keep in mind the variance in MMC3 IRQ counter behaviour literally took years to figure out (over the course of almost 2 decades). Just some context. What I'm saying is, it doesn't surprise me that a quirk of this nature would exist for a long period of time.

I'm not interested in Nestopia fixes though.

As I said, check $2006 writes x IRQ clocking/triggering. Stuff at $52xx registers might be interesting too.