This is something I intend to start testing carefully. I was in the habit of getting a new amp, listening to it "straight in" for a few days just to get a feel, then throwing my loop pedals in the loop, and my "front" pedals in front. I always really liked my Mini Rec but was loving the V25 so much I decided I'd sell the Mini. I had it boxed up, ready to ship. This is not a good time of year to sell gear, and it sat, so the other day I got it out and was just like "WOW that thing sounds great. I had plugged my pedalboard out into it but hadn't put the loop pedals in since they were attached to a different amp. I played it for three days last week and basically decided I wasn't selling it. Then we had family over for Christmas this weekend and I plugged the loop, pedals into it and was playing and it just didn't sound as good, I figured, because I wasn't turning it up very loud because there were 20 other people at the house. Tonight though, I'm going to crank it back where it was last week, and plug and unplug the loop pedals to see what I hear. Maybe it was the volume... but maybe it's the loop pedals.
(FYI- The only things in the loop pedal setup right now are TC Dreamscape>TC Flashback>TC Arena. At one point I had an MXR 10 band at the end, but it was rarely used so I unplugged it. Also, I intend to through a buffered boost pedal in there and try it in front and behind the other loop pedals).