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?
Unmodified SCPH-77006 with SM 3.6
SCPH-39006 with M-chip modchip, SCPH-10281 NA and refurb Seagate 80GB HDD
SCPH-10000 v1.00 with SCPH-10190 PCMCIA NA and SCPH-20400 HDD unit