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When was the last time this machine was shut down, or at least restarted? You'd be surprised how effective they can be a fixing common weirdness.
I restart the computer every night, but that doesn't solve the problem.
After some more investigation and reinstalling Matrox's software several times, I discovered the source of the problem. If the computer goes to sleep power supply to the mxo2 is cut and when the system wakes up again the card won't work until you shut down completely the computer and restart it again (except when the system goes to sleep with AE open). That also happens when you change the output from AE to any other option but Matrox's. By now the solution is to avoid that the computer goes to sleep, but I don't think that is good for the machine is it?