Alright, this issue should be simple enough:
Whenever I build the crafting unit, any valid size, it works just fine at first.
I can use it as expected during normal usage, but it stops working once I restart my server.
This seems to be a MultiPlayer specific issue, as SinglePlayer I can leave the world and re-open it and it still works.
Once it stops working it won't let me open the GUI or craft anything with it, like its not even there, until I completely break every block of the machine and re-build it all completely.

Minecraft: 1.12.2
Forge: 14.23.1.2590 (It also happens with all versions up to 14.23.1.2605)
RebornCore: 3.6.4.194
RebornStorage: 3.0.3.36
Logs: No logs appear that are relevent to RebornStorage beyond normal loading logs

Does this happen after you log-out and then log back in. Or when the server is restarted?

I did further testing, it seems to happen every single time the chunk is unloaded, the server restart I am guessing is mearly just a cause of is unloading, it is leading me to guess something is wrong with saving the structure itself or re-initializing it when the chunk is loaded again. I should let you know I do have the cubicchunks mod for infinite world height and 16x16x16 chunks, but I tested removing it and making a new world without it, and it did the same thing for the crafter, becoming unusable when it is unloaded

It turns out it was an issue with my specific system, as even the same .minecraft copied onto any other computer are not having this issue, and a re-install of my system fixed it, so closing this issue.