Hi Thorsten,
The 3 settings that you mentioned are set properly. When I turn off optimization I am able to get more reproducible results (hitting the same key gives the same midi code, and I can hit the same key more than once and get a midi code). Now I only get "note off" messages when the keys are released. There are no "note on" messages and nothing happens until a key is released.
It looks like I have my wiring mixed up somehow. I am now getting note off a-1 (90 15 00) when I press key E-2 (but only when the key is released, nothing happens when the key is fully pressed (as an aside, isn't midi status byte "90" note on for channel 1?)). From there, descending chromatically I get the sequence leading up to E-2 when I press a-1 (i.e. pressing D#-2 gives "90 16 00", pressing D-2 gives "90 17 00", and so on until I press a-1 and get "90 34 00".
I have a schematic for the keyboard and the two connectors for the left and right sides are labelled identically to those shown on the Fatar DF 88 diagram on the midibox site, so the wiring should be straightforward. I think I am going to have to trace some wires from the keys back to the DIO_MATRIX board to figure out where I have gone wrong.