steps to reproduce:
Get chest full of redstone and/or silicon and pipe it with enderIO conduits to top slot of etcher. Etcher shouldn't accept both of those in middle slot.

possible solution ideas:
-lockdown of slots, to only accept locked item
-leave 1 item to reserve space
-disable redstone and silicon in middle slots (like they're blocked in top spot in AE inscriber)

oh, whoops. should be a quick fix