Ahh, seems like this is due to my harddisk image not being correct for this.

The hd image is different between using an A3 driver with the CFFA2 card and Apple2 Prodos using the CFFA2 card. The Apple3 one has partition info in the first block which seems to confuse the prodos block mode. When I make up a nice new hd image of two 32mb disks it at least boots ok now :-)