The system stopped working again earlier today so I broke and replaced the controller. It was still broken afterwards. /=
Something I did do the other day was make a new folder with new server files, and transplanting the world/properties/banlist/ops, and enabling the mods we had enabled like powerconverters and hats. We still had the problem afterwards, so I can only assume it's the world somehow breaking. Maybe I could upload the world somewhere and have someone look at it.
As another problem, having quarries put items into a tesseract to my AE system wasn't working, the items were spewing everywhere. The tesseracts were all set up correctly and it was still accepting items from my plant farms, base set to receive, farms/quarries set to send all on the same freq.
Oh also the tesseract in my base goes into an interface.