You have ended up with two configurations for WinSCP, Windows registry and the INI file.

Now, where do you have more data/settings/sites stored? In the Registry (that you were using prior to running WinSCP as Administrator) or in the INI file (that you have started using by running WinSCP as Administrator)?

If in registry: Just delete (or rather move it away) the INI file (while no instance of WinSCP is running).

If in INI file: Go to Preferences > Storage > Configuration storage and select Windows registry. You still get an error about the INI file. Then close WinSCP and delete the INI file (move it away).

References:
https://winscp.net/eng/docs/config
https://winscp.net/eng/docs/ui_pref_storage

Hi there

I set up a workspace in WinSCP, after having started the program using "Run as administrator" in Windows 7.

Now if I ever start WinSCP in normal (i.e. not admin) mode, when I try to close the program it prompts me to confirm, saying "My Workspace" will be automatically saved. However, if I click OK, it comes up with an Access Denied error, and I can't close the program.

Have attached images showing the confirm dialogue and error.

Cheers,
Jeremy