I think you'd have to troubleshoot a little more. Maybe something is drawing the signal down for some reason? Do you have TMCC/Legacy engines or powered cars on the rails?
Remove them to test. I bet you need chokes on them.
Can you disconnect the TIU totally from your layout and try hooking up 2 spare pieces of track, one to channel one fixed and one to another channel. Then try to power both with a single MTH engine on each.
I have a feeling your layout is back feeding power from some where? Did this issue just pop up? Did you just change any wiring? Do you have the polarity correct on all channels?