I've always lost tone in an effects loop. I have no idea why the effects can't pass the dry tone without messing it up, but they manage it. For some reason bypass modes are often the worst--unless the unit has a hard bypass (ie, engages a relay to physically skip the unit) the suckage is intolerable.
I finally gave up on the loop thing. I have a rack full of flashing lights, so I took the final out from the preamp (this won't help if you have a combined head, of course) and ran it into a rackmounted mixer. I feed effects from the mixer's aux sends, setting the effects for full wet, and bring the results back through the mixer's other channels. I set the levels for the effects through expression pedals on an Ultrafoot.
A lot of work, but I can have effects AND tone and set the mix on the fly. It's nice with the expression pedals because I can choose the effects between songs, setting the mix to zero. Then the effects are there, just not in the mix. When I need one, I can fade it in or out with the expression pedal. Since the dry signal never goes through the effects, it's unchanged no matter what effects are used.