Suddenly AVR32 Studio V2.6 has started working better. It is now possible to debug where previously the system would hang all the time or take several minutes (if one was patient enough to wait) for the debugger to jump over a loop.
What helped? Executing AVR32 Studio V2.6 as administrator causes it work quite diffently. It does need the projects to be imported again (as administrator it starts with an empty environment even when there were several projects imported when opening it as a regular user) but then things started working which had never worked correctly before...