I also just started having this issue. I have two NC2IOs.
Unit 1 is version 7-8-220728 Mark D, and set to "Genlock to External Video Clock (SDI)" (No idea why the sync menu options changed between versions)
Unit 2 is version 7-7-211105 Mark D and, set to "Genlock to External Video Clock"
They are both connected to the same video router (Evertz EQX), switcher (Ross Acuity), and sync source (Evertz 5601MSC). Unit 2 works great, but Unit 1 will only output on up to four of the SDI outputs. The working outputs change every time I switch between "Internal System Clock" and "Genlock to External Video Clock (SDI)".
I was hoping that rolling back the software (if possible) might fix the issue, but considering the age of this thread it doesn't look promising.
Has anyone made any progress on solving this?