So, some friends and I found a server some weeks back called Break Out. Interesting concept: you start in a padded room and you have to break out, wherein you find successive layers harder and harder to break through. One of the mods the pack revolves around in Applied Energistics 2, and so my friends built a massive ME system that fills up the entire base (not as large as you'd think, spans probably three chunks in each cardinal direction...and it was tonight, weeks after I'd been gifted a copy of the world to play on my own, that I discovered something funky going on with the ME system. Specifically, there was one Molecular Assembler/ME Interface combo that just didn't want to hook up to the system, despite the fact that the former machine was online. I've found a fix for this: break and replace one of the cables leading to the bank of Molecular Assemblers.
The problem lies when I then exit the world and return; it matters not if I reload the entire modpack or just log/relog, the same thing happens. Upon returning to the world, I find that I have to break and replace the cable again to get that one Assembler/Interface combo reconnected. Mind that the Assembler is online the entire time (apart from when the cable is disconnected).
Is there any way I can fix this on my end, or is it a bug they have to fix in the mod itself?
...and once again I've been too quick to give up on myself. I've found the solution, and it's incredibly simple: a bit of reconfiguration of cables and Crafting Storage/Monitors and we're off to the races.