This sounds like it could be a “dual scan” issue, not an issue with BatchPatch. Please review the following links very carefully. Let me know what you find.
Definitely still review your settings, and in the second link it shows how to see if “dual scan” is actually enabled regardless of what group policy is in use. The problem you are describing really does not seem like an issue or problem or setting with BatchPatch, which has not changed, and which is not causing a problem for any other BatchPatch users.