I've seen such problems my self, and it's not because of drives spinning up. I've set my disks to never spin down, and they never do.
I get this small freezes in Theater View. It's mostly when I navigate to other views, but it have also happened a few times while navigating thumbnails. The whole MC is locked in this period of a few seconds, and I think that doing things like button presses or mouse clicking can make MC go gray in "unresponsive" mode. If you wait patiently a few seconds it all kickstarts again and the remaining button presses is registered, making lots of jumps through views or thumbnails. This is on a fairly fast and new ASrock HTPC, so I do not think it's the machines fault. It should not be the drawing of the new views as this is normally very fast. The HTPC is on a wired LAN, so it should not be the connection either. It happens perhaps every other day, and I've just coped with it for now. It's not a good feeling, but it don't hurt my user experience noticeably either.