My entire applied energistics network is contained within one compact machine, with several compact machines inside of that holding some of the larger items. One of those holds my interfaces and assemblers for autocrafting. This has been fine for several days, but recently I've noticed that crafting a single item will take up to 4 or 6 seconds per item. This lag also applies to any import buses on my network, which will take 4-6 seconds per pull, even if there are still items left to take.

My power supply to the network is fine, and the assembler is powered/online, it just freezes at 0 or 10%. I've tried connecting an energy cell to the offending assembler with no results. However, when I placed an interface/assembler combo in the same compact machine as my controllers and drives, they worked flawlessly.

At this point, I've tried profiling the server to no results, but due to the empirical evidence, I do believe it to be an issue with compact machines itself.

Here is the 'outer' compact machine. The gold compact machine with the saturated dense cable holds my interfaces.

And this is inside said machine

And finally, one of the assemblers in question. (This one will freeze at 50% because of the acceleration cards)

UPDATE:
After some more investigating and some help from the AE devs, I've narrowed it down to the fact that Compact Machines doesn't seem to remove GridNodes when they're supposed to be. I've been watching the grid and node count for a while, and it's steadily rising, causing serious lag on the server.