I won't be able to give you any technical info, but in one former playing situation I used to use a Kustom Quad 100DFX and plugged my Tech 21 Sansamp into it. When I tried to plug into the effect return I got lots of noise and clipping and other crap, but if I just put it in front of the amp with the amp set to clean, it worked great. I eventually read other accounts of the effects loop being noisy on that amp, so my point is that it's not unheard of for effects loops to be noisy.
I'd personally start by cleaning out the effects loop jacks with some contact cleaner like DeOxit. If that doesn't work, you might want to do some googling to see if that's a common problem. If it is, you might run into a solution for it or you might just end up not using the effects loop very much.