Ian,
Given that you're a longtime user of PG Music products, I suspect that you've already tried the below. Just in case you haven't, though ...
It sounds like the "Merge to mono" option is electronically engaged even though it mightn't be checked. (See image below.)

What I'd try is the following ...
1. Do a merge with this option selected. Then do a second merge with the option unselected. That might just give it a kick to reset.
2. Failing that, I'd reset RB to factory settings by renaming the REALBAND.INI file and RB.CFG to something like REALBAND.INI.OLD and RB.CFG.OLD. This will effectively "delete" those files so that RB is forced to create new ones (thus the factory rest). If the problem is not solved by doing this, you can always delete the newly created files and then return the original files to their original names.
Hope these thoughts work,
Noel