I have created a simple extension which I managed to upload to the Visual Studio gallery without any issues.
When I however updated the extension and tried to upload it again I got the error message "Your VSIX ID already exists on the site" even if I updated the version number (tried updating from 1.0 to both 1.1 and 2.0). I'm probably missing something but I thought that the VSIX ID identified the extension itself so only version should be changed when uploading a newer version.
I have checked inside the .vsix package and the files within reflect the new version number. So I've now run out of ideas to test.