--- Quote Start ---
I did also try Modelsim and that is nice and fast for functional simulations but what I really needed were timing simulations. It seems that I'm clocking some parts of the design too fast and in other parts not waiting long enough between feeding input and reading output. None of these problems become apparent in a functional simulation, there everything works
--- Quote End ---
You should catch this kind of problem in static timing analysis if you entered the timing constraints properly. Timing simulation doesn't catch all the problems that static timing analysis does. As I mentioned before, see Rysc's comments about functional versus timing simulation at the end of
http://www.alteraforum.com/forum/showthread.php?p=13315.