There were some problems with the analog to digital conversion board (the Demodulator).
Basically the sound input did not match expected bit output. And since we're fresh out on oscilloscopes, the next best thing was an USB sound card, baudline signal analyzer and a test signal composed of a start bit, all zeros and, stop bit and half a sinus wave for debuging:
From this it was discovered that for some reason the audio signal was inverted and (since WAV files shorter then 5 milliseconds weren't recognized as audio clips, so the rest was filled with silence) that the start bit should in our case be composed of two bits, first one setting the threshold to one and the second one to zero, so that the transition from hight to low will be registered (since it obviously does not from zero to low). Probably the same thing should be applied for "stop bit" as well.
All this means the audio samples containing bit info have to be regenerated and then can the module be retested.