Zoltan - you are experiencing a problem with the offending app(s), not Windows 7. In time, the developers may adjust their apps to use the current (or correct) Windows APIs, but in the meantime, I think you have to deal with it.
As a workaround, you could try changing the view. Or opening files through Explorer instead of the app. Hopefully, the offending apps will force the file to open in the already running instance, and not open a new instance.