hey RG - try using 27c020 or 27c040 eproms and doubling up or quadding up the PRG rom data for the prg rom with the following commands on your commandline:
copy /b ntrq_ntsc.prg+ntrq_ntsc.prg ntrq256.prg
^ gives u a 256kb image for 27c020
or for a 27c040 eprom:
copy /b ntrq256.prg+ntrq256.prg ntrq512.prg
Hope that helps! (it could be to do with higher address lines and possibly some nes board layouts being funny about small 128k eproms, I saw this behaviour once before when I was putting my first NTRQ cart together...)
Can you let me know if that cures the issue?
Cheers! \o_
PS as long as you use the ucon64 command -s and take the .prg file it spits out you are okay re; ines headers etc...