Hi everybody,
even if this thread is quite inactive, here is what i found out about this problems. Apparently you need to make sure that all inputs and outputs related to the JTAG interface are constrained, especially the clock. This has been the answer given by Altera when opening a service request. After constraining this aspect of my design i didn't experience other bugs like this. So it's worth checking.
I hope my answer will help others, this problem being very rare apparently and i didn't see any other answers concerning this problem.