Yes I only file from the E-file center and only highlight specifically what I want to file.  I literally did exactly this with the agent witnessing.

I can't see ANY circumstance where the programmers should allow the entire return to file when only extension is highlighted in the e-file center regardless of what boxes are checked or unchecked. IMO this is a defect in the program that  should be addressed and fixed. 

Thanks again for taking time to reply.