Family table instances become standalone parts when saved during assembly use

When using family table instances within an assembly, the assembly requires that the instance be checked out in order to perform a save. The instance is somehow being modified, perhaps by dependencies, or otherwise. Once the instance is checked out, and the assembly is saved, the instance is no longer a part of the family table, and becomes a stand alone part. This is causing major issues with family table versions if the instance then gets checked in.

I have created a video to demonstrate what is happening as an example: http://communities.ptc.com/videos/2206

The S741.prt instance disconnects itself from the family table when the assembly using the instance is saved. During the example I've only done an edit definition, without changing anything, in order to save the assembly. I cannot figure out why the behavior to modify any of the parts used in the assembly is happening, as nothing has changed.

Both S740.prt and S741.prt are a part of the family table generic VOS_BODY.prt. I am able to checkout the VOS_BODY.prt and instances and make changes without the instance becoming Standalone. The instance remains intact to the family table. However, when checking out the instance required for the assembly operation, this is when the instance becomes Standalone

Has anybody else run across this at all? We are using Wildfire 4.0 M200 and Windchill 9.0 M050.

Thanks!