Your loop is probably parallel, meaning the dry sound and the loop sound run side by side and mix together at the return pot. A parallel loop is meant to be lightly mixed in with the return knob and the pedals should be 100% wet for this (mix at 100%). Make sure your Send knob is at Noon when beginning. Turn it one way or the other by a small amount until the sound of the loop on and off are about the same.
The alternatives are:
Have the return maxed out and set the mix on your pedals. The Send still balances the volume between on and off.
Modify the loop to serial. This eliminates the dry side-chain and removes the filtering effects of a parallel loop. However, the loop has to always be on for the amp to work at all.
2007 3 Channel Dual Recto w/loop mod
My Humble Music Tech Blog: Dual Rectifier Index