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My application connects to different databases. The connection strings are saved in the user settings. I cannot use the application scope because the data is changed at run-time.
If the user starts the application normally there is no problem. However, if he uses the "Run..." command from the Start menu then a different folder in User\AppData\Local\MyApplication is created containing a different user.config.
Is there any way to stop or bypass this behavior?
This behavior cannot be avoided.
It seems that Windows does not identify programs started by other programs as the same as programs which are run by the user.
To solve the problem you have to avoid settings made by the ConfigurationManager and create your own files to save data as pointed out in the comments.