Sadly, BoW was right.....
Contra is unplayable at the 3rd level. This goes for all clones as well. Graphics become completely garbled after your first jump.
EDIT: I have verified that I have the correct rom for Metal Slug 5 with the correct M1 information. I have the same Metal Slug 5 that Kenshiro has, yet his works and mine doesn't.
I've deleted all config/save files I could find in all FBL folders and it still doesn't work.
Is there any hidden TDATA/UDATA I need to find too?
EDIT2: Since I can't figure it out I'm just going with the AES version that works for me. According to this page, the AES versions were identical to the arcades, so we're not losing anything.
http://www.oldschoolgamer.ca/node/112EDIT3: Kenshiro has fixed 5 out of memory errors so far, bringing the grand total of working FBL games to 720 unique games.