Ok, think I know part of the issue.
The base 15 missions don't prefix the hero-specialist names, but Desert Seige prefixes theirs with c_, and Island Thunder with a d_. I went in, and edited the unlocked_hero subdirectories to reflect this, and it appears to have remedied my initial problem, but...
I only get the 'authorised' specialists in the expansions, and I want everyone available everywhere. I guess this means I have to not only duplicate the hero directory from OrigMiss to MP1 and MP2, but the Kit and other associated files too (or merge them, rather?)
Perhaps this is more mod