I'll post it in both areas.

I used the shift+crtl+F8 method.

Okay, the problem seems to be the same in hardware and software rendering.
Could actually be a PCSX2 problem then..

I was playing with the presets and changing the settings to "most harmful (6)" the issue appears resolved.

I'm not exactly sure what specific option was changed, but whatever. There doesn't seem to be any side effects what so ever so I'm not inclined to, by trial and error, find out what fixes the bug.

Thanks to everyone who tried to help me <3

try different combinations of the cycle rate sliders

VBA-M

And please attach your memory card, so I can check this out.
It's important we investigate these things