I suppose that this should have been mentioned in the FMCB guides, but since I don't think it was: FMCB should not affect the playability of your Playstation 2 games.
If your console has a modchip, you might have to disable it.
@OP: What if you booted up your console without your FMCB MC inserted? Will the game run properly?
SCPH-10000 S. MINOKAMO v1.01 (Defunct)
SCPH-10000 S. KISARAZU v1.00 (faulty)
SCPH-15000 S. KOHDA (With warranty seal!) :D
DESR-5100 S. EMCS