Really WEIRD problem! App open, but not open!

Hi, I'm on OSX 10.6.8 Snow Leopard. I just came across a super bizarre problem I've never seen before! So I have an open document TextEdit. Only the TextEdit icon in the dock doesn't have the little indicator saying it's open, and if I right click it, it shows the option of Open. The open TextEdit document shows the menu bar options like normal, and I can use it like normal. But I can't close it from the dock because it already shows it as closed! I can only close the document from the menu bar. Also, I can open an new TextEdit document from the dock - but again, I can't close it from the dock, and the dock icon doesn't show it's active. In Activity Monitor, it shows TextEdit as active with 2 threads.

What's going on??

EDIT: I just noticed the same thing is true for iTunes! I'm playing iTunes, but the icon in the dock doesn't show it!

Thanks. I think my dock was corrupted, because when I opened an app that was not in the dock (from the applications folder), it would never appear in the dock.

Anyhow, I restarted, and the problem went away. Disk Utility doesn't show anything S.M.A.R.T status shows as "verified". I repaired permissions, but it didn't do anything, only the restart fixed things. Hope my HDD is not failing

Never had this issue before.