To enforce games/programs to use a particular video mode, you should use the "GS Mode Selector" (GSM).
It can be found and downloaded from a thread here.
As for your problem with some homebrew software not accessing your disk properly: Some homebrew software use an older USB mass storage device driver that do not access some USB disks properly.
The only solution for you is to either wait for the author to update the software, or to get another USB disk that can be accessed properly by the software.
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