Does using the registry disturb the use of settings?

I've tried rebooting and it makes no difference. The purpose of writing to the registry is to make Windows pass the filename of a doubleclicked file as an argument.

I don't think the linked thread is relevant for the problem I'm experiencing. All settings are saved and retrieved as I expect them to apart from the detail that I end up with what appears to be two sets of settings. When I start the application from the Start menu it reads from and writes to one set. When I start the application by doubleclicking a file the application reads and writes to a different set.