I forgot to add this, but this was already done a year ago when I set up the machine.
To 6:
There where Multicore issues in the past with NI plugins and also with UAD in conjunction with Cubase.
To me this seems to be the most likely cause. Again, this machine with the same components used to run without any hiccups for nearly a year. Software updates (no new software) were the only changes that were made during this time and the problems started with v6.