Okay, so trying to repair the installation of 1.1 didn't do anything, and not being able to uninstall Paint.NET 2.5, I deleted it from the Program Files folder. I cant install 2.6 beta now however as it still thinks 2.5 is installed.
I have tried to remove the reference to Paint.NET 2.5 from the Add/Remove programs list in the registry (HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\Uninstall), but it isn't listed in the registry. Would anyone know where its stored?