V6 is only used to amplify the return signal and does not govern the output level on the send. The Mark V does not use a fully tube buffered FX loop. The send level or attenuation is created by transistors which is part of the 5BEQ summing amp. What is the send level set too? If you are getting distortion or signal degradation from the FX loop are you using an effect in the loop? To diagnose the issue use a patch cable from Send to Return, there should be no signal change unless the send level pot on the rear is set to a lower value. However if you are using an effect on the loop, it needs to be line level compliant otherwise the signal will be overdriving the input buffer on the effect resulting in compression, clipped or distorted signal or tone loss. You may need a line level shifter placed in the loop that drops the send to a lower level and then re-boots the level back to line for the return. (devices of similar design generally do not require a power supply as they are mostly level shifting transformers). It is not stated in the manual or specifications what the FX loop level is. I had problems with most of my old gear that was all instrument level, I could not use any of it in the loop. There are a handful of products that will work on line level (+4dBu or higher). If the manufacture does not specify a signal level maximum ratings on the product, chances are it is instrument level -20dBu). I have no clue what the Mark V signal level is on the FX loop send, but I have had great success with Strymon pedals in the Mark V loop and they work equally well with the other amps as well as on the front end with the guitar signal. Boss Terra Echo 2 works very well in the loop too. Line6 DL4 and TC Flashback both degrade the signal with my Mark V FX loop, Line6 tends to compress and muddy up the tone, I get static like noise with the TC flashback and some distortion on the clean channel. Those are the only two pedals I have since I got them to replace my old gear only to find they do not work as effective as I wanted them too as both are great delay pedals. So far in the Strymon line up that I am using without issue is the Big Sky, DIG, Brigadier, and Ola chorus.
If you are comparing the hard bypass to the FX active (with the FX loop turned off by foot switch or rear control panel knob) there will be a difference between the two drive circuits since the masters of each channel are driving V6 which is part of the global master volume control also includes the solo function.
