Hmmm... I couldn't recreate this bug in my testing. Bobsmods works. Bobs + Angels works. Miles + Bobs + Angels works. I'm assuming you're not using shiny mods, so I didn't test with those. Must be something else affecting the vanilla machines that makes the copy fail?
Because having the same recipe is what's supposed to happen; the Balance option just makes the mini machines an exact duplicate of the base machine, without changing power use, module slots, recipe, etc. But they definitely should still be smaller. The only reason they wouldn't be, is if something changed the original machine to something my copy function isn't expecting.
Unless you have it disabled through a mod, you can also hover an entity in-game, and it should tell you what mods are affecting. Try checking them again, and see if some other mod might be affecting the vanilla assembler and miner?