Part on the fly incorrectly system generated into parts master

We use parts on the fly within our Job BOM’s to represent sub-assemblies where necessary. Upon marking a Job with this structure a template, this Job is then copied (via get details) into Engineering Workbench after the fact to better revision control the BOM. The unexpected result of this is that Epicor automatically activates all of these sub-assembly parts on the fly and makes them activated parts. This bypasses the BPM we have to restrict part number logic, as well as generates demand. Has anyone else seen this? Is there a setting we can turn off to keep this from happening?