Update: It appears that even after I redefine the faces that it makes me redo it the next time I edit the BC. Even if I don't change anything, editing the BC requires a face selection to hit OK and close.
unfortunately this is a known issue with 2012 SP4.0.
even if your file was brand new in 2012, if you edit the definition of an input, the faces will be lost.
I believe that I saw that it will be fixed with 2012 Sp5.0.
The only workaround is to X out of the edit definition command, that will keep your selections.
Please contact your reseller to report this issue and add your name to the SPR so that you are notified when it is resolved.