Alright, so the issue was that I have a check to make sure none of the ingredients have a count > 65535. I also have a check to make sure the results don't exceed the stack size (since in such a recipe anything above the stack size just disappears). But I don't have a check to also make sure results don't exceed 65535. Normally, since stack size is usually way below 65535, this has never been an issue since the check I do have is usually more stringent.
In this case we had both a stack size larger than 65535 (stack size of coin item is 1,000,000) as well as a recipe that, when applying the 50x multiplier tries to produce > 65535 as a result. So it passed my check, but failed the game engine's 65535 limit.
This issue will be fixed in version 0.1.6 and the mods now load together.