Why is my tone altered when I run a BOSS-ME50 through the effects loop?

I have a Mesa Boogie Triple Rectifier, and I am trying to run my ME50 through the effects loop just for delay. It sounds fine through the clean channel, but when I turn on channel 3 (dirty channel) it sounds like there is a ton of flange on, even when everything on the pedal is disabled. Why does this happen, and how can I fix it?