This should be fixed in 1.2.3. The game starts normally for me, but I didn't test every configuration yet.
There was a special case when adjusting existing productivity techs where I forgot to include the check for valid labs. In this case "dark matter refinement productivity" required nanite science packs which can only be used with the special lab, but that one does not allow for the basic science packs anymore (automation, logistic, etc.). At some point, I'll need to think of a way to dynamically react to weird science pack progressions/labs from mods. But for now, the mod just ignores them.
Please test and let me know if V1.2.3 works for you as well.