And lets start with the obvious, YES! I feel stupid!
Thanks to everyone for the input...replaying everything over in my head, trying to figure out how this was possible, it finally came together. In my original post I said "At some point, probably around the following weekend (4/27) I added a second box of foundation". I didn't have an exact date on this because I didn't have it recorded in my records, but "assumed" (yes, I know, a dangerous word)....it had to be between my 4/20 and 5/04 inspections and I had just forgotten to document it.
However, what really happened was this....As I mentioned it was a large swarm, so I originally hived them in the two boxes. A second box was never added, they had it from the start. I confirmed my suspicion by confirming in hive tracks that I had it configured with the 2 boxes from the beginning.
Therefore, when I confirmed a laying queen on the 4/20 inspection, that was in the second box, not the first. I never went down to the first box...ever. They were drawing comb and she was laying in the second box so I "assumed" (there's that word again, :() the same was happening in the first. In hindsight, it's now obvious that they simple never worked the bottom box to any degree.