I'm not quite sure I understand what you're asking.
When you start your computer, does it have an error pop up that something cannot be found?
It may just be a deleted file, and either your registry is looking for it on startup, or your startup menu has the deleted file referenced to it.
You probably don't have a clue what I'm trying to say. Anyway, more detail about what "Run/run program" is would be nice, or maybe even a screenshot?
