I reproduced your issue by following your settings. The BB synchronizes to the looper MIDI after recording and immediately playing back the loop. After powering down the looper and BB and then trying to play, it went into the pitch-changing mode.
I am able to get it to stay in sync by changing the settings on the BB pedal to
- press Drum Set and Tempo to enter the settings menu
- scroll to and select Main Pedal
- scroll to and select Midi Messages
- select MIDI-OUT
- scroll to and select Sync
- change to Disable and back out of the settings
This may also resolve the problem you posted to Intro does not synchronize with looper