I believe it's a directshow/thumbnail building problem. I'll be able to direct you to the correct thread, I htink. I was at work before, so not enough time to link you then. Just re-read your post, and I htink it sounds like my problem. Ignore the specifics i.e. Haali if you don't run it, but tell me if it sounds like this:
Could it be a 'building thumbnails' problem?
Most of my videos use Haali as a media splitter. One 'feature' of this is that every time it's used a little tray icon appears. I've noticed that when MC becomes unresponsive, my system tray is filling up with Haali icons. This is usually indicative of thumbnail building. When this happens, right clicks are not registered, the scroll wheel doesn't work and drop-down menus don't function either. Trying to tag any fields causes them to exit from editing mode. After a minute or so, the system becomes responsive again, but there's no knowing how long (usually a few seconds) one has to complete the task you were trying to do before the freeze/shut out starts again. A simple task such as copying a thumbnail/cover art to clipboard could take three minutes or more while you constantly right click to see if it's done yet, is it done yet, is it bloody well done yet?
I get similar behaviour when I request a thumbnail build, even though it's meant to be done in the background. However, I notice that the little status area in the lower left of standard view doesn't always tell the truth. Once it's said it's done building, it's actually continuing to make more, as judged by the Haali icon in the tray continuing to appear and trying to quit MC results in a notification that thumbnails are being built. If I re-request to build missing thumbnails once it claims to have done them all, there are somehow hundreds or thousands left to build, even though it claimed to have done them all a few minutes before.
I've found that each time I request a thumbnail build there are fewer left to build when the task starts. I'm hoping that once the process is over finally, that the freezing/shut out problem will go away. I disabled all my Symantec anti-virus software last night. I got the feeling that the shut-outs were shorter in duration, but they're still happening for sure.