Just as a note, in almost all situations, I find that line levels are quieter and I was more than a little surprised that, in my setup, this is not the case with the factor pedals. However, this is just my experience with my system. Bottom line, use whatever settings work best and sound best for you in your rig.
Neo, my original reply was simply meant as a rough troubleshooting suggestion. Basically, just trying to isolate the problem. Once you figure out exactly where the problem is, it'll be easier to fix.