Win 7 64-bit home premium, and DOTA 2 is the only game that I recall ever doing it. Of course that and Portal 2 may be the only games I have with the new update method that presumably copies like 5GB of files locally, modifies them, and copies them back.Are you still on Vista? I have never had that happen on Win 7 64-bit.
Another weird thing about DOTA 2, every other game you can remove from the update list by clicking the X once it's done, but for DOTA 2 you almost always have to completely close Steam or it will just stay there. The X doesn't do anything.
I think I only have an old 7200 rpm hard drive though, so I really need to back it up and get a new one.