Can't locate entities in files from the Project Navigator in Quartus II V10.1

I submitted a SR Feb 25, but no response as of today on this problem, so I closed it and resubmitted. Maybe it will get to a different person.

I've always been a little leary of changing the "top-level" entity to compile different parts of a circuit. Of course this can be very useful and should work robustly, but I've had unexplained problems in the past (all the way back to Quartus 5) that seem to occur when I do this. I even wonder if the problem I'm experiencing now is related to doing this.

GN