Applications not starting

When I startup certain applications -- the more RAM they use, the more likely it is the problem will appear -- they stall mid-startup, or slow down to the point where they are effectively stalled. The program will show up in the "processes" tab of task manager, with the CPU hovering around 50% and memory usage increasing veeery slowly, but will not appear in the "applications" tab. There are no other resource hogs visible in task manager, viewing processes from all users (cpu about 50% idle If I leave it going the application will eventually start -- after 20-30minutes (not exaggerating) -- and will then run with heavy performance issues. If it takes longer than that to start, I've either rebooted or stopped the process.

This doesn't happen all the time. Sometimes all applications will start fine (and run very nicely when they do) but often they won't. And once they have stopped working I have to reboot to get them going again.

I have not been able to recreate this problem while superfetch is disabled. Which isn't to say that it wouldn't happen, or that superfetch is the cause. But disabling it seems to have aleviated the symptoms so far. Obviously I'd rather keep superfetch on.

I have 4GB of RAM, Intel Core 2 cpu 6600 @ 2.4GHz, and a separate hard drive for pagefile (which doesn't seem to ever get used because there's always heaps of RAM). Both hard drives are new (with a new install of Win7), and everything else is at least 6 months old. I try and keep everything clean with frequent ESET and Advanced System Care 4 scans. Drivers are all up to date, etc.

Any help would be hugely appreciated.