Hasta La Motion!

i sometimes have scripts, that seem to run in some kind of endless loop. Usually, when the script runs smooth, cpu usage is barely at 50%. But sometimes, cpu usages peaks at 100% as shown in the taskmanager, yet nothing happens! I can see some nodes blinking in the DAG, but no process at all in the viewer. And believe me i have waited long enough to make sure that really nothing happens. This is very annyoing as it seems to happen very random. Has someone had similar behaviour?
I have a Intel Core 2 Quad at 2,67GHz with 8 GB Ram.