I’m guessing it’s a phase issue, I’m just not 100% sure just how much latency each block is actually adding, which would be very useful info for NDSP to provide. My best suggestion is recording both to separate tracks and zoom in to see how much the phase is off and adjust until it’s close. Ideally, I wish the QC had some kind of compensation option, either some kind of algorithm for automatic phase compensation or at least a sample accurate delay, but for now, your best bet is manually moving the tracks after recording. If you’re just blending both signals on one track, then there’s not really much of an option at this point other than adding more blocks, but again, we don’t know just how much latency is added for specific blocks, so it can’t ever truly get to the point where it’s almost perfectly in phase.
When using dual amps of any sort, you have to address phase. If the amps have a different number of tube gain stages, or a different approach to the power amp phase inverter, they could be out of phase. For example a Fender Twin Reverb and Fender Showman both using the Vibarto channel will be out of phase. You have to introduce a phase inverter in the signal chain somewhere and try flipping the phase to see which sound better.