I can't really test too many cases, but from what I've tested, it seems that Gotlag's Electric Furnaces will tend to load before Bobs Assembling Machines, meaning that the recipe changes from bobs mods will overwrite the simple recipes from Electric Furnaces.
This is probably because Electric Furnaces has no dependencies, and is probably loaded on the first pass (at the same level as Bob Library, which is a requirement for Bobs Assembling Machines, meaning that it would have to load on a later pass)
Should be fixed as of v6.2.5, where I've removed the incompatibility check between Gotlag's Electric Furnaces and Bobs Assembling Machines.
Apologies for the interruption to anyone's ongoing games. I just don't like dealing with random crashes, due to multiple mods overwriting each other, and then the game points to my mod as the problem.