I have been using a regular Beat buddy pedal with an Electro Harmonix 1440 looper pedal for about a year with no problems until recently. I use the BB (latest software and firmware upgrades) to control the tempo and midi start of the 1440 looper. It has worked flawlessly until now 
What’s happening now is that the looper pedal is not playing back the correct Pitch that the loops were recorded at. Midi start and stop commands are fine. Pitch is somehow being transposed way off base. Useless to me! I’m clueless here and thanks for any suggestions.
It sounds like your looper playback has gone into variable speed. Can’t tell you much more than that as I don’t have an EHX looper so you’ll have to check your looper pedal settings.
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I’ve been having the same problem. If I got from creating a loop with no external clock, then ever turn on the external clock, it seems to permanently overwrite the loop to a different pitch/tempo.