Same for me: Turning "Background tagging of other files" = False helps some, but I still run into long hangs (less often) where SE is unresponsive (cursor on Win7 is the swirling circle, app window is frosted/dimmed, title bar says "not responding") for anywhere from seconds to minutes. When it stays stuck longer than a couple minutes I kill it because I need to get back to work.
Also, now that I'm paying close attention to background tagging, I frequently see many "invalid file seek position" errors on the status bar while SE is tagging in the background. The files where it reports that are perfectly valid files that exist and which SE is able to tag just fine, so I'm not sure what's going on.
I'll open the zip file from Matthew and see if his settings help further.
By the way, I'm using SE mostly on solid state drives, so I'm a bit surprised there are any perceivable hangs at all. I don't think SE is blocking on IO, the IO is too fast for that and there's no seek time. So I'm hoping it has something to do with the size of batched operations or something, and that Matthew's setting tweaks will help.