There are two possibilities.
The first, less likely, possibility is that there is a soft error somewhere
on your hard drive, and it's preventing GS/OS (actually, the SCSI driver)
from the reading some necessary information from the second partition. If
re-installing GS/OS and the High-Speed SCSI drivers doesn't solve the
problem, you probably will have to reformat the hard drive.
The second is slightly more likely: Some Applied Engineering cards use the
DMA channel to move information. The IIGS has only one DMA channel, and
the High-Speed SCSI card may be fighting the AE card for access to the
channel.
Here are two things to try: Either turn off the DMA access on the
High-Speed SCSI (DIP switch 1) or remove the AE card completely from the
system and then test. I believe that Applied Engineering has an update for
some of their memory cards to deal with this situation. If you find that
this is the problem, try contacting them for a possible fix.