First, I must say, the problem you observe most likely not because of a ROM. Ofcourse thats just my "hunch"
But since you already started to re-program them let me share some of my experience with EPROM burning;
- If the EPROMs you are dealing with are old, take the time to clean their legs with a metal brush. A dremel metal polish brush works great (but don't dremel it, just use the tip manualy)
- EPROM burners we use are generally low quality cheap ones (at least mine are so

) and their ZIF sockets gets rusty also. Clean them with metal brush like you do on EPROM legs.
- When you lock the ZIF socket after insering the EPROM, force the EPROM a little (few milimeters left and right) with hand side ways. This will agitate the contact point between legs and zif socket and if there is corrosion there it will sanded away. Believe me, it may sound stupid like blowing to NES cartridges

but works for me if I have read/write/verify errors.
- Old eproms sometimes not get erased easily especially with cheap chinese eprom erasers. I generally clean the glass window on the erpom with a cue tip dipped in alcohol or acetone and give good 30-40 minutes. If that doesnt work the chip may have long gone. Just use another fresh one, especially a newer CMOS type as
@stj said.
If after this you manage to burn the ROMs and you still have glitches. Just share couple of photos which may help us elaborate more. I suspect a faulty logic IC in some part of object addressing stage may have faulty output. But thats just speculation for now.
Regarding your questioı about region set. I think they would all work. Japanese version is mushc harder, thats what I've heard.
