I had a problem the other day with my Tacx Fortius and I actually forgot that I had had the same issue just after I had bought it. The trainer would work fine when cycling and then suddenly the rear would start braking in a erratic way. Almost braking and then releasing with small jerks.
After some googling I found that it was quite a common fault with the Fortius units and all it was was just the connector plug that had some loose wires. Below are some photos of how to fasten these again.