have you unchecked preserve aspect, and check full screen and put in 1920 x 1080?
I did that before and I even ran bootleg another time with different settings and still have the same problems (no materia in menu and missing whatever is below config, game can not run in fullscreen).
For what it may matter, I did get 2 error logs this time around:
ealin_2 patch failed, not original script
frcyo patch failed, not original script
and
blin67_2 patch failed, not original script
chrin_2 patch failed, not original script
cosin1_1 patch failed, not original script
ealin_2 patch failed, not original script
elmin4_2 patch failed, not original script
elminn_1 patch failed, not original script
games_2 patch failed, not original script
gongaga patch failed, not original script
goson patch failed, not original script
kuro_4 patch failed, not original script
lastmap patch failed, not original script
min51_1 patch failed, not original script
psdun_2 patch failed, not original script
Couldn't encode world_us.lgp: Incompatible filename
I do not know if these are what are causing my errors or not. It's all just jibberish to me really. Normally I would fix errors like this by just cycling through settings, but it takes a very long time simply run bootleg through again (and have to extract everything again) so I'm just sort of hoping someone else may know, or has fixed the problem before.