Posting in case someone else runs into this same issue. I'm running a Mark V 90w in 4CM with a Fractal FM3, and found that channel 2 was giving me some phase issues in the FX loop. IE, dry signal bleeding "around" the FX loop, partially out of phase with the FX signal, causing loss of highs, weird cocked wah tones, etc. I read a few other guys having the same issue, one of which commented that you just need to turn the channel volume up. That actually does work, however it also adds a lot more gain and makes it more difficult to balance all three channel volumes. Another guy said you need to repeatedly flick the hard bypass switch on and off. Weirdly, that seemed like it worked too (at least for a while), but seemed like not a very good actual fix.
I contacted mesa support about the issue. They acknowledged that it does happen from time to time, citing all kinds of variables like signal trace variances/spacing, FX loop cabling, etc that can all contribute to picking up stray signal. He also said sometimes a tube may not be as good at keeping the signal discrete from triode to triode. Looking at the schematic, V6 is shared across the channel 2 send and the global fx loop return. Long story short, I replaced V6 with a brand new tube and the issue is now completely fixed. You can check this by just running only a tuner in your loop. With the tuner itself bypassed, you should hear no signal. If you hear a low volume signal, you're getting some bleed. Swapping V6 should fix the issue. Hope that helps someone.
I contacted mesa support about the issue. They acknowledged that it does happen from time to time, citing all kinds of variables like signal trace variances/spacing, FX loop cabling, etc that can all contribute to picking up stray signal. He also said sometimes a tube may not be as good at keeping the signal discrete from triode to triode. Looking at the schematic, V6 is shared across the channel 2 send and the global fx loop return. Long story short, I replaced V6 with a brand new tube and the issue is now completely fixed. You can check this by just running only a tuner in your loop. With the tuner itself bypassed, you should hear no signal. If you hear a low volume signal, you're getting some bleed. Swapping V6 should fix the issue. Hope that helps someone.