Another possibility: since you say you can get into the Control Panel go to the Control Panel and select Slots, look at the Startup Slot setting and make sure it either says Scan or 5, which is the Slot for the 3.5 drives. If it doesn't say Scan or 5 change it with the arrow keys to one of those two settings.

The Apple IIGS expects to find 3.5 drives in Slot 5, 5.25 drives in Slot 6 and hard drive controller cards in Slot 7. There are more possibilities but the important thing is to let the computer know where to look for a disk to start up with.

Dean