Possibly Solved. Cause Unknown.
I am having the same issue removing certain extensions. eCart at the moment. What I found was that every time it said a file was in use, I opened the folder and there was one or more temp.tmp file (if more than one it would be temp1.tmp, temp2.tmp...)
If I delete this file, it gets by the message and removes the file. When it happens again repeat.
These temp files were created now, so it isn't a left over from dreamweaver running. It is something in the removal process.