my P4 hasn't got hyperthreading as far as i know, also the new version of gpxpatch gives as with that new function where you can choose the computer or something like that, options to choose "all, 1" and not "all, 1, 2" (i understood that with hyperthreading you could choose the cpu, so i think "all, 1, 2" has to stand there when you have hyperthreading)
it are all random things when it happends, sometime it's by opening another file, sometimes when you switch to another application and then go back, and sometimes it's just when you are moving the circuit. Theres as far as i can see no perticular reason that it happends.