I'm sorry I don't have any answers for you, but my hive is doing the EXACT same thing!!! I'm hoping someone will have some insights. I am a 1st year beekeeper & was quite surprised when my bees swarmed instead of moving into the lower box!
Now they're building comb on the top bars of the bottom box & building up! I just don't know what to think other than my bees didn't read the Warre manual! I'm glad to hear I'm not the only one experiencing this.
Keeping my fingers crossed that both of us will get some suggestions. Good luck!