IIgs ROM 3 8 MB RAM (I think) via a special card in the auxiliary slot High Speed SCSI card (rev. B I think) - Slot 7 Unidisk Controller Card - Slot 6 Hard Drive - System 6.01 installed 2 x Unidisk Drives (hooked up to the controller card in slot 6) 2 x IIgs 3.5 Drives (hooked to the smart port)
For trouble shooting/testing, I'd suggest you remove all the cards and drives from your IIgs except for the disk drive card with drives and reset all the defaults in the control panel except slot 6 and 3 set to my card and speed set to Normal and try it again.
The IIgs then becomes a plain old enhanced IIe with 128k ram. Run the self test at this point, OpenApple-ClosedApple-Control-Reset(IIgs, keyboard, monitor, disk controller card, dual floppy drives, default control panel settings except slot 6 and 3 and speed set to normal.)
Then try any software you are having issues with. If it boots in an 'enhanced' IIe, it will boot in a IIgs with a drive controller card. No exceptions that I am aware of.
If the software works, add back a setting and/or periferal at a time until you find out what makes it stop working.
Thankx, Ed