Matthias,
I have seen something similar. Did you create any DAQmx task or channel definitions in your project or did you create them in MAX?
In the case of a co-worker, the problem was the project based DAQmx channels and he had to blow away the project based channels and recreate them in MAX. The problem was verified by NI tech support but I never did hear anything about a fix.
I would suggest creating a very simple vi that uses part of your DAQmx code and run a couple of experiments. First verify that the small .exe has the same problem. If your original vi used project based channels, then try redefining them in MAX and see what happens.
