I'm going to make an educated guess here - are you in a PAL region but booting an PAL-patched NTSC game? That might account for the screen position issue (without a Y-fix performed, PAL has 96 more scanlines than NTSC and so there will be 96 black lines below the image). If so, GSM should be able to work with that, but I would recommend going back to the original disc and letting GSM handle the video mode.
Chip-free/MC-free homebrew <3
FMCB 1.93 on MC for emergencies, NA
250GB HDD/FHDB 1.93/OPL 0.9.2 (GSM and non-GSM)/PS2 games, NO HDDOSD
80GB HDD/FHDB 1.93/POPStarter rev12/OPL644/GSM0.37/PS1 games, NO HDDOSD
SCPH-75001 (sitting idle, slims suck):
FMCB 1.92 on MC