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When I right-click a file in windows, and choose 'Textpad' for the file to be opened in, the file *ISN'T* loaded in an existing Textpad session, but in a new Textpad window.

I recently upgraded from 4.6.0 to 4.6.2.

Have you checked the General Preferences?

Click on Configure, Preferences.
Remove the check mark from the box "Allow multiple instances to run".

Click on Apply, and OK.