Transitions cut out guitar??

Hello: Moving onto other matters… I have my Boss RC20 XL in line prior to the beat buddy and running the looper’s output in the the mono input of the bb. The mono out of the bb goes into a voice doubler’s through- put to a channel on a acoustic two channel amp.
I kept thinking that the guitar had an issue or the battery was bad as it was cutting out, not just staticy, simply no sound. I tried a second guitar and the same thing happened. Then I began to notice that this was happening when I held the bb main pedal down to transition to the next phrase. The guitar would re-sound shortly after releasing the bb pedal. So to test further I turned the bb volume down so there was no sound interference and held the pedal to transition, sure enough… when I hold the pedal to transition to the next phrase it cuts out the guitar… is this possible… am I missing something? Could this be certain songs only… I can’t see how?