Well; umm.. I guess pull your Pi out of the OS Board put some header pins (Ray sent me some with my OSBo) or jumper wires in the same pins connected to the OSBo and using a multimeter see if your getting any output (3.3v DC) with all the stations enabled.. verify output is gone with stations disabled.. This should verify your Pi is sending a signal. Sorry I dont have a pi so I dont know exactly what pins your looking for but it shouldent be too hard to figure out.
If your pi is sending a signal than its likely the OSPi board is faulty; if your not getting a signal out the Pi either you have a software issue or a faulty-pi