Unfortunately that's how it works – out only tramsits info generated by the first box, thru only passes info from your midi footcontroller. A "midi merge" setting would fix our problem (v4 pretty please!).
If your footcontroller allows multiple CC's to be sent from the same footswitch, you could have it broadcast a CC n one channel for the first box, and a CC on a second channel for the second factor. Unfortunately, I'm short one channel for CC's on my controller (FCB1010 Uno). Its possible with the right footcontroller and careful planning though.
Outside of that, perhaps think about a single footswitch attached to both boxes' aux switches just for taptempo.
-joe
