I can tell you right away it definitely had that Issue before too. This Issue is stupidly complicated to explain, but it all depends on completely random circumstances like which Item IDs each Item has, which means if one Mod just adds one more Item (like GT6 did between the two updates) it can fuck over the whole System.
The real Issue here is that CoFH-Core was made in the most incompetent way possible, resulting in this Issue happening only when Factorization is installed for some dumb reason, because of its Acid Bottle doing something weird with its Hashcode. (yes I remember having that Issue years ago…)