Hello gillatgh,
Yes, it is a bit strange but it's not brain surgery, right?
I no longer believe the Lexicon MC12B is the source of your issue. It seems, in your current setup, you only use its internal dac chips for ht processing and you use the 103 for cd playback connected directly to the Rogue.
However, I'd still suggest removing it because it's unnecessary and using the 103 for surround decoding, and connecting its outputs directly to your 5 ch amp, will likely be a significant improvement for ht sound quality and it'll streamline your system to just the necessary gear.
Once you get the time to reconfigure and setup the 103 as the 5.1 processor, there are some other features on the 103 you can explore.
Things like the audio processing setup screens where you set the size ('small' for sub assistance or 'large' for no sub assistance) and relative volume of each of the 5.1 channels, the cutoff frequency for bass sent to your sub and how you want 2ch stereo cds to be processed and outputted. You could get a head-start on this by reading these sections in your 103 manual.
I'll monitor this thread and await updates.
Tim