I did a few test uploads and it looks like two things a few things are happening and the file uploader is trying to compensate for the changes. For example, I've noticed all my public galleries are now visible in the archive folder dropdown.
When I try to upload to one of these galleries, PM uploads it to that gallery, no problems.
If I click on "New archive folder" and try to send it to the newly created folder on PS. It ends up in the pre 3-24-12 archive section of my account.