(Wasn't totally sure if this should be here or on the Minetweaker tracker, but hey, it's about mod compatibility.)

Like the title says, using recipes.remove() on a Mekanism recipe doesn't take effect on session start, but only works after using "/mt reload". remove() is the only way I know of to remove "Mekanism Shaped/Mekanism Shapeless" recipe (in fact, if this info helps at all, removeShaped() doesn't work; it has to be remove()).

Hmm, maybe mekanism adds some of its recipes after minetweaker executes the scripts. Can you post the command you are using?

val digiMiner = <Mekanism:MachineBlock:4>;
recipes.remove(digiMiner);

edit: with the appropriate brackets on the val assignment of course, idk how this github formatting works.

Mekanism adds recipes after the world starts, therefor, mekanism issue. A mod is NEVER meant to do that, with minetweaker excluded.