Does the server have the same ID's for the Adv. Machines as the Clients? Otherwise it might be a Code bug. I'm not sure, I'll look into it after the weekend.
Last thing I can suggest to help with the problem is maybe changing it to a Red Power 2 based system with Sortingmachines and Pneumatic Tubeing. Maybe the SMP code of BC (Maybe even SSP) pipes isn't up to scratch to sort that much info at once. I can remember a Plugin which would let you see what was Ticking a lot on your server but can't remember the name at the moment. Will look it up in the near future.
Also try to stop all the items in the pipes by stop putting stuff in them, maybe that will stop the lag a bit. It looks like you have A LOT of stuff running through them, and that can't be a good thing.
NullPointerException in my experience happen when the server has a different ID for the items you are trying to craft then what the client has. Check that your ID's match.
Go into your Tekkit folder (found in Windows %appdata%/.techniclauncher/tekkit/) then go into the config folder. It's either Enderchest on ID 177 or Alchemical Chest on ID 177 change that to a unused ID (I think 122 is free) and try again.
Crystal chests show the items inside the chests, somehow I think that 240 chests are a bit too much for your/any PC to handle. Try it with diamond chests.