I think I just figured out what the problem is. I started looking into EmonLibCM and I noticed in the documentation it specified it supports up to 5 CTs. So having run out of other ideas I tried nuking the 6th CT channel and BINGO! it is now working.
The precompiled firmware works fine with all 6 CT channels so I guess someone must have updated EmonLibCM to support 6 channels. But it seems the update was never pushed to github.
Edit:
And there it is…

A full day of troubleshooting boils down to a single character fix xD