Running stereo into 2 amps - are some M13 effects potentially making signal out of phase (polarity)?

[jcfay]

HI all - I recently started running stereo to 2 amps from the M13, using the 4 cable method.  It sounds fantastic, but the other day I noticed a few modulation effects (if I recall correctly it was a chorus and a flange) when triggered led to a significant decrease in volume output.  I've had no other issues with a uniform volume coming out of the M13 (into a Fender Hot Rod Deluxe and Suhr Hedgehog, FYI) until that day.  I don't use any compression, distortion, fuzz or overdrive (none of the "yellow" category) since I use the front end of the amps to generate distortion. 

 

I need to check and see if the amps are actually in phase as setup (I've also got a volume and wah pedal in front of the M13, and a digitech jamman looper after the M13) - I think they are but will check later today.  But what I'm wondering is if any potential combination of effects that can be generated on the M13, and then run through a stereo setup, can they lead to a phase/polarity issue? (I assume not...)

 

Thanks!