I have seen this myself but not too often and I was never able to pin down anything specific causing it. Sometimes the issue can be fixed with some cleanup. Besides cleaning up your version if windows (temp files etc) there are 2 folders in the bat's mail folder that can cause slowdowns. one is "cache" and you can clean that one right out and "imgfiles" which contains all your downloaded graphics from HTML emails etc (not attached graphics)

BTW What version of The Bat are you using?

If you have any questions, post back. If you need a good cleanup tool google Ccleaner and Wise care and pick the free versions