I think DoctorQ has it there - had a very similar issue myself. (although my icons were in the top left :-P)
As he says, the BPPCfix output opens a CLI before P96 initialises; this causes workbench initially to open on a native screenmode, then redraw when the monitor drivers initialised. As the icons are initially drawn on the native screen, their positions (defined with refernce to your P96 1024*768 - or whatever - screen) are invalid. Thus they are drawn all bunched up in the top left corner.
Try "BPPCfix install >NIL:" (iirc - the install bit might be different, it's been a while).
This will send the bppcfix output to a null console, thus the first screen which opens will be your P96 Voodoo workbench screen.
Voila, icons in the right place.
