Okay I've tried to replicate the issue, was not able to but ran into a quirk which may explain what's happening with you. Windows is VERY FINICKY. You cannot MAP the same COMPUTER 2 times with different logins.
so if you've connected to the remote computer using Windows Explorer or the Run command, then you've already logged in with your own credentials. If MCEBuddy now tries to connect with your supplied credentials it will FAIL since Windows will reject it.
So when you drag and drop the files, you're doing it with you OWN already mapped credentials and it works fine, when MCEBuddy tries to scan the directory with the configured credentials it fails (check your MCEBuddy.log).
The answer to this is simple:
1. Either use your own credentials and MAP the remote computer folder using Windows explorer and DO NOT enter any credentials in the Monitor Task or Conversion task pages for that remote computer. In this case MCEBuddy will use the Windows Explorer credentials.
2. DO NOT map or connect to the remote computer, instead enter the credentials in the MCEBuddy Monitor Task and Conversion Task page and let MCEBuddy connect to the remote computer.
Remember you CANNOT do both above, otherwise MCEBuddy will not be able to access the remote computer.