Ok, it seems to boil down to some issues we found while developing the cart, let me explain:
It seems some pce/coregfx models are really noisy inside and the digital signals aren't too "clean" and sometimes have glitches large enough to be picked as a different logic level by the level shifters. Old, slower hardware is more resilent to that noise, but fast modern hardware can pick them unintentionally when sampling the signals. The FPGA program tries to filter and ignore any glitches found, and needs the signals stable in order to accept them (as a read or write) but maybe it still needs more tweaks.
It took a long time to make the code resilent to those issues, but it's something that can be fixed in firmware, now we just need a way to reproduce it, as the current firmware was tested to be glitch free in all our consoles (my 4 coregfx, 4 pce, 1 sgx, 1 tg16 + the ones Alex has) and our testers'.
What I found is that the consoles with more issues were also the ones with more jailbars and rgb noise, so all this seems to be related to something inside the consoles that wears over time (maybe capacitors). That doesn't mean you need to change anything, we'll fix that in firmware, it's just a general comment about the current state of the ageing PCE consoles

. I have 4 PCEs, and initial firmwares worked great on one of them, the one I used for development. One day, I switched to other one, and arcade card failed randomly. It is what I call the "cursed PCE", and my main development one ATM

. It has strong jailbars, it's yellow decolored and smells of cigarrette smoke. I haven't been brave enough to open it, fearing what I could find inside

.
Also, on a side note, having a region mod installed probably adds noise to the data lines because of the longer and unsielded wires of the usual mods will pick more noise.
Why it affects only to Arcade Card? my guess is that there are some random read/write signal glitches that happen sometimes (also I've seen the CPU repeat a read or write for no apparent reason, probably pipelining) but they don't affect the game as there aren't usually any side effects and reading or writting twice the same address in the SSDS3 is mostly harmless (that's not really true, especially with cd registers, but they are very filtered and accessed slowly, but mostly is) but the arcade card, as every read or write to the data port increases the reading address, an erroneously repeated read or write causes a big difference, shifting the data, and causing severe graphic glitches.