there is a known bug report when creating a new configuration with flexible sub assemblies. when you create the configuration, then select parent/child options to create the config in your subassemblies, if one or all of them are flexible, it will suppress the individual parts inside the subassemblies.
This was reported with 2009 sp0.0 and is still in 2010 pr1.
It is easily duplicated. Create a few subassemlies with a couple parts a piece. insert those subassemblies into a master assembly. change any of the subs to flexible. Then create a new config in the master assy, make sure to click parent child options and click on the other subs, so the config will be created on all of them. The flexible subs will have their internal parts suppressed while the subassy itself is not.
Not sure of where to submit info for PR1 so if you know, please post it so I can send in another bug request.
Thanks for looking