Oh boy. What have I gotten myself into. Entanglement and everything that establishes some sort of connection rather than stores stuff in a buffer is kinda broken. This includes Applied Energistics as well as OpenComputers.

Problem is that each entangled CM is using the same GridNode in the overworld. But each entangled machine should have its own instance for several reasons (e.g. because all CM blocks belonging to the same room all lose their GridNode when one of them is being broken, none of the remaining is connected to the AE system anymore - they all lose their connection).

There are several solutions to this problem:
a) Get rid of the entanglement feature. It is overpowered and does not really fit the concept of the mod to begin with.
b) Do a twisted version of the SharedStorageHandler allowing for multiple instances not only depending on the coord+side combination, but also on the actual "entangled CM instance".
c) Rewrite everything, you know a lot more by now and everything could be cleaner and prettier and shiny and actually nice to work with. Sigh.

My vote is on a), but I will think about it some more.