Hi there, maybe someone has my same problem or maybe I'm wrong.
I installed WP 3.2 RC 2 on a sub-directory called "newtheme", not directly on the root. On the root I already have a directory called "mytheme" with a previous version of WP.
In "newtheme" installation I'm trying to upload a zip file with a theme called "mytheme", but I can't because WP says to me that a directory called "mytheme" already exists... I think he's talking about the directory on the root, but it is a different installation, very strange as far as I know. Maybe a bug?
The upload folder is the default one. Sorry for my bad english, I hope this explanation is quite clear ;-)