Drew
Is this the case?
No. The software uninstaller should do more. It all depends on how well the programmer has written the uninstaller.
You can manually remove redundant startup entries using Autoruns. You use Autoruns to delete entries where the words “File not found” appear. With Autoruns you can uncheck an item, which disables it from starting, or you can right click an item and then delete it. Click the Everything tab and look for the rows highlighted in yellow.
To identify what loads when you boot use Autoruns (freeware from Microsoft).
http://technet.microsoft.com/en-us/sysinternals/bb963902
With Autoruns you can uncheck an item, which disables it from starting, or you can right click an item and then delete it. If you uncheck you can recheck to re-enable the item. It is a much safer approach than editing the Registry and better than using msconfig.