Thanks for acknowledging it is a software issue. If it helps, I have this problem also and here is what I tried (unsuccessfully).
I did a complete uninstall including removal of all FTB files in the Program Files (x86) and Program Data directories. I renamed the MyHeritage directory. Then tried a fresh install of the latest version and started it to create the myHeritage directory. Then I closed FTB and copied my .zed file into C:\...\MyHeritage\Nishimura\database\Nishimura.zed. I then restarted the program and opened the project. I am still not able to merge even from a site that I am a member of.
Let me know if I can help by running some test cases as a Premium user, or if you want someone to test a patch or revision prior to general release.
I must have recently hit my smart matching limit. It would have been nice to know that there even was a limit in the first place. I would have considered this when deciding whether or not to upgrade to a PremiumPlus account. I've also wasted a lot of time trying to figure out what was going on through the forum.