Anyone? :/
It sort of sounds like a problem I have, except that I think I know the reason for mine.
I have an old HDD in my system that came into existence around the time SATA was first introduced. It has both an IDE and SATA port.
Ever since I've switched to a new MB that doesn't support IDE anymore, there would be random pauses (10-30 seconds) whenever a program that was located on that certain HDD was run.
I'm using Windows 8, so I can see that the active time shoots up to 100% and the response time is in the >20000 ms range whenever that happens.
I've grown to assume that the drive doesn't properly support reads/writes/spin down in SATA mode and that's why I get random pauses all the time whenever I run anything from it that requires constant access.
My solution was to move all the programs off of that particular drive and treat it as a storage drive instead.