*Windows Vista and 7 specific*

When I edit netbeans.conf file with PSPad, which isn't running in Administrator mode, the changes are saved into Virtual Store, instead of the file's original location in Program Files folder. IDE then runs with this changed configuration.

Installer dosn't seems to check for Virtual Store when uninstall is started. This behavior have two impacts:
1) When user changes default userdir, installer offers to remove the userdir from the original netbeans.conf, which can be invalid (used by another installation). In case it doesn't exist, nothing is offered for removal. In both cases the actually used userdir isn't removed.
2) After uninstall, the changed netbeans.conf remains in the Virtual Store. When a new installation is performed, IDE will use this file, instead of a clean one that comes with the installation. This results in unexpected behavior (e.g. different JDK is used, than the one selected during installation)

I don't know about any other situation which results in the use of Virtual Store than editing netbeans.conf with PSPad. Windows Notepad doesn't allow to change the file this way. I'm not very familiar with the way how Virtual Store works, so I can't estimate how many users can be affected.

Still, my suggestion is to check during uninstall if there is any configuration in Virtual Store, take it into account and remove it afterwards. Also maybe check for it during installation and overwrite it if there is any.