ZENWorks Patch Management Server 6.4 SP2
This issue is caused by the use of Source Groups.
When a Custom Group is using a Source Group all devices in that group get added to the Custom Group. Removing them using Group Management does not remove them from the Custom Group, because the Source Group still contains those machines.
To modify the Source Groups used, or disable the use of Source Groups entirely, follow these steps:
1. In the ZENWorks Patch Management Server page go to the Groups tab
2. Right-click the group to be modified and select Settings
3. On the right-hand side there is an Other section. Click the Modify button to the right of Source Groups
4. Modify the Source Groups as appropriate and click OK