Hi Mihael,
If I remember well, Stäubli had Molex PCU-DPIO (or PCU-DP2IO) board and not PC104pfb board.
Make sure you are using a PCU-DPIO board.
Applicom IO software shall detect board installed in stäubli controller under condition that you create a 'remote configuration' with correct IP address.
Try to use ApplicomIO v4.2 or 4.3 and select menu 'Erase flash' (don't rememeber exactly where it is located) before initializing.
Best regards