I don't have access to a JVM410 to test our M-series devices with here in Support.

But I do use an M9 regularly in several musical ensembles I record and perform in outside of work. My preference is to run the M9 in front of tube amps: the ones I have access to are an Orange Tiny Terror and a DT50 currently. I've also run the M9 in front of a Vox AC30 (my favorite so far).

In all these cases, the delay models in the M9 have never "boosted" my instrument level signal unless I sweep the feedback amount for noise/self-oscillation type effects, but that's not the same as a "gain boost". I run it in "DSP Bypass" mode.

After the M9 I use a Z.Vex Box 'O Rock but not in the manner most might. I have the "Boost" circuit turned on always, but use it to buffer my signal and in some ways, "limit" the threshold to a set knob level. It changes from show to show (depending on the amp gain settings and how the amp sounds in the room). It has a "distortion" circuit that I have the Drive set to minimum, but it still acts as a gain boost for leads with the Tone filter circuit to help.

So in a sense, the Z.Vex pedal is a level adjustment device that I like to run after the M9 for more gain/buffering options.

Still, I've never experienced anything like you've described where the Delay effect(s) of an M-Series unit boosts the guitar signal more than say, a Tube Screamer. There's no gain boost in the Delay models (aside from a few models that offer Bass/Treble controls).

Have you tried re-flashing the system software of your particular M5 using MIDI cables and Line 6 Monkey? I would do this next, since our devices are firmware (software) driven: http://line6.com/support/docs/DOC-1632