This is a wierd issue I recently ran across. I was using remote debugging and I needed to copy over the PDB symbols file to the GAC. I used the command line to copy the file over to the appropiate location. I ran the command line down to the folder I needed to copy to in the GAC and left it open since I didn't want to write that out everytime I needed to update it. (I know I'm lazy, I should of and ended up writing a BAT file to do it for me).

With it left open I noticed that when I updated my solution it would fail and not deploy my assembly to the GAC. I realized that this was because I had the command window open to that folder. I didn't think that it would matter since it wasn't doing anything but sitting there. I closed the command window and re-deployed to my web applications and everything was fine after that.