I had a similar problem when I first transferred my 3.1 install on 2.5" Hard disk from WinUAE to real Amiga.
I plugged the Disk back into my PC, reduced the Maxtransfer Rate in HD Toolbox via UAE and it worked after that.
Good advice.
Also as others have said, make sure you have 3.1 ROMs. If not, use a Blizkick type tool to launch the 3.1 ROM from the first line in the startup-sequence.
