Have you tweaked the relationship between the amp's Send, Return, and Loop Active Master knobs? The Loop Active Master knob might be the missing link here. From the Mesa web site regarding the Loop Active Master knob:
"This knob of a different color, works in conjunction with the FX Loop Select Rotary Control that is found on the Rear Panel in the FX Loop section of the amplifier. When the Loop is switched out of Bypass the Yellow Loop LED next to this control comes on with the channel in which the loop is active. When this LED is illuminated the Loop Active Master replaces the Channel Masters to become the overall Master Volume Control. At this time the Channel Masters become channel balancing controls and Effects Loop Send Level Controls. This LOOP ACTIVE MASTER Control also serves as an effects Return Control and can be very useful when trying to use certain older effects with weak output capabilities."