This may be one of the most interesting bugs I have encountered in my coding career. TL;DR everything is my fault: my remove productivity option causes an infinite loop only if there are more than 1024 recipes with productivity enabled.
There is not actually anything special I changed that caused this bug to happen (it was in here from 0.17.1) or anything special about omnimatter, it's just that you happened to exceed this limit of recipes with productivity and then this bug that had been dormant became active and froze the game. Fixed for 0.17.6 (ignore the typo in the changelog).