Most notably the recipe conflict between AE2 energy acceptor and Iron Chests copper chest upgrade.

Trying to do this in a crafting station or with the AE2 crafting terminal usually gives the chest upgrade, but it seems to be somewhat random what you get.

I'm not sure if you can do anything about the recipe selection button, but it might be a good idea to go through the crafting recipes and remove any notable conflicts.

Problem occurs on both 1.1.4 and 1.1.5, not sure about older versions.

https://www.curseforge.com/minecraft/mc-mods/polymorphic-energistics was invented a week ago
also a version for refined storage https://www.curseforge.com/minecraft/mc-mods/refined-polymorphism

Yeah, polymorph doesn't work in all crafting table like block entities. The final solution and the most clean is to remove duplicate recipes. I'll do this.