Facing the back of the amp, just left of center there should be a cluster of rotary controls. They are from left to right: FX Assign, FX Send Level, FX Return Level, Footswitch.
The FX Assign will tell you whether you are using the FX loop at all and in what manner. Set to Footswitch...the FX loop is engaged only when you hit the FX button on the footswitch as far as bringing in anything connected to the loop. Having it set to anything other than Bypass means your Master Output and Solo controls on the front are active and are a part of your volume equation.... as well as now your FX Send Level is part of the equation. Make Sense?
It is easy to experiment and get a handle on what controls are active in what setttings. There is also a stencil next to the Loop Assign knob under Loop Bypass that states Defeats Output and Solo controls (when set to Loop Bypass).
Set your Assign to Loop on, Ch1, Ch2, Ch3 or FTSW and turn the FX Send...you will see it effects overall volume.
I also might add that from some recent experimenting...the FX loop does effect tone. When I bypass the loop all together the amp seems a bit tighter and more dynamic and 3D sounding. But I like to put the FX to FTSW so that my Output and especially Solo controls are active because I like the Solo button for lead volume boosts. Even though I do not run effects in the loop, I still keep it set to FTSW....I just don't actually activate it.