AE2 autocrafting ore-dict substitution don't work for diferend types of wood (Vanilla planks =/= Rubber wood planks), if recipe is with oak plank it will not make jungle planks from rubber wood. You have to make recipe for it from jungle wood.

This is yet another issue opened that's just a misunderstanding of what Substitutions does in AE2.

Substitutions will allow existing compatible items to be used but AE2 will never autocraft anything but the exact items specified in your patterns.