What I typically do is boot from 3.1 floppies and partition(don't forget 0x1fe00 maxtrans) and install WB 3.1/PFS. Make sure it boots, Then switch the card over to my PC and go from there with AmigaForever/UAE and install ClassicWB or 3.9.
I have never had an issue taking that additional step, however I have run into the same type of issue just UAE from the get-go. Also that method allows me to do the FastATA split thing to see multiple 4GB drives.
Hope that helps...
