Hey, Neo! I think your problems may have to do with a level mismatch, but let me ask a few questions first…
It sounds like the problem is more pronounced on the distortion channels, they are always noisier than the clean channels, but is there any increase in noise in the clean channel as well when you use the TF in the loop? It wouldn't be very significant, maybe almost unnoticable. Since the loop on the JVM410H can be active for any channel, if the problem is only on one channel, it may be the amp. I doubt that, though, and am guessing you'll hear a slight noise increase on all channels.
Which loop are you using? The JVM410H has two loops, one "serial/parallel" and the other "power amp insert/serial"… Either will work, but I'd guess you're using the "serial/parallel" loop so you can turn it on and off with the Marshall's footswitch or channel memory.
If you are using the "serial/parallel" loop, what settings on the amp are you using? What's the FX Level? What mix are you using? If you're using less than 100% wet, do you have the TF set to DRYKILL?
Just to make sure, you said that you're running the Decimator before the TF, right? That's good, because if it was after the TF, the changes in level due to the echo repeats could cause the Decimator to let more noise through than it normally does.
Loop Send >> Decimator >> TF >> Loop Return
Try disconnecting your Decimator or at least leaving it off temporarily… I know this will be noisier, but what I'm curious about is whether the noise still increases when turning the TF on and off when the Decimator's not part of the picture. Just trying to make sure that the problem isn't in the Decimator by removing it from the chain.
Finally, what are your level setting on the TF? I'd try setting both switches on the TF to "Amp/Guitar," the amp's loop level to -10dBV, and the loop mix to 100% wet. (The TF's DRYKILL should be OFF in this case.) While the "line" setting on the TF seems appropriate with a loop level of +4dBV, in my experience, this can be noisier and may be where your problem is.
That's about all I can think of right now… let us know if any of the above helps, or if not, exactly what your settings are and we'll see if we can get this one figured out for you.
