Problems with Clone Theory in a split signal

I'm running my effects in a Boss LS-2. Channel A is just my OC-3 octave pedal while Channel B is my Nano Bassballs, my Bluebeard fuzz, and my Clone Theory.

If I run Channel A with the OC-3 off (as a clean signal) and the Clone Theory by itself in Channel B with the other pedals off, my signal drops a LOT. The volume is fine running with Channel A turned off and going straight through the chorus.

Is the LS-2 blending of the Chorus + Clean causing a cancellation of some kind?

 

There is no problem with the volume if I run with the Clone Theory off.
There is no problem if I only run the channel with the clone theory and don't sweat blending.

On a possibly unrelated note, I was playing with the Stereo feature and ran the main output from the clone theory into input A of my amp and the stereo output into input B of my amp. Merged, the final sound ends up being "sounds like there is no chorus on." I wondered if it might be related.

For the time being, I've pulled the Clone Theory out of the LS-2 loops. Wish me luck.

 

Thanks y'all - I had never run into phase problems before, but read about them here all the time. It was the first thing I thought but I didn't want to assume anything. For now, I am playing with a stripped down pedal-board that eliminates the OC-3 and the LS_2 - considering I did it for acoustic stuff, I really should yank the Bluebeard too, but I feel like messing with the band a little during casual jams.

Running both Clone Theory outputs to the same amp was just for fun - At some point, I'll run to two amps, when I have the time and opportunity to get either both amps at home or both amps at practice-location set up next to each other.

Thanks everybody!