By 'Both Channels' in Dual Parallel with the 1/4" output, I mean the 'right' and the 'left' output.
(There is no difference between 'top' and 'bottom' on each side.)
Try the right side, and then the left side - they should sound the same with the Balance centered.
What's your EQ like ?
"Flat" on an LH1000 is typically 2-10-2. IOW - Treble and Bass almost but not quite at zero, Mid all the way up.
If you're running with everything at noon you have a significant bass and treble boost.
I have, and have used, that exact setup - LH1000 into HyDrive 410.
Ahhh.....I will check into that ASAP later today.