When you have access to the AmigaDOS Shell, type this:
Ed S:Startup-Sequence
And see if that Alphagen program is in there, instead of all the regular Workbench startup stuff (ending with LoadWB). I think the best thing for you to do is move everything in the root of the boot drive into a temporary drawer, then install a fresh copy of Workbench 3.1 on there.
Do you have any way of getting files onto the computer apart from floppy disk?
