In my Arc Hydro training with ESRI I was told that, when things start going "funning", get out of ArcMap, go to your temp directory and delete everything you can. Then start up again. This has cleared things up for me many times.
In Windows 7, mine is at C:\Users\mboucher\AppData\Local\Temp. You can tell if this is where the ESRI program puts temp files, by opening the folder, sorting by date (new to old), and starting ArcMap. If this is the right directory, you will see temp files being created. There are some that you can't delete while in other programs so you may have to close all programs to delete all the files. There was usually one that I could not delete. It's name became familiar and I assumed it was related to Explorer.
This was such an issue for me at one time that I had a shortcut of the temp directory in my tray and opened it all the time to make sure ArcMap/Arc Hydro wasn't frozen.
Hope this helps.