Well I had a lot of other stuff to get working before I managed to do something with this adapter. But found that I had trouble when using the HSMC_TX_D_P[9?]. This is assigned to the same pin as nCEO. I remember reading something about this but I could not remember the solution. After about 30 minutes I remembered having a similar problem with another board once (I beleve it was the DE2-70) where a pin was configured as a programming pin.
So for others who encounter this and immediately search this forum:
1. Go to Assignments->Device->Device and Pin Options...
2. Open menu Dual-Purpose Pins
3. Set nCEO from "Use as programming pin" to "Use as regular I/O".