I believe the quarry was my fault, in the desert if it's what is referred to. I hadn't thought of that until just now, thank you. I will need to look at it ASAP.
I did turn off the quarry itself when I wasn't on, for several reasons (one being the chunk load for one, two being waste of power, three being the waste of blocks as they spat out with a full chest anyways).
Since I'm on the topic of chests, do we know if the lag regarding crystal chests from Tekkit is also present in FTB? I don't have source quotes, but I know several Tekkit servers I play on have Crystal Chests disabled. I'm not sure on the exact specs.
Getting back to the water thing... two questions:
1) What tips can folks offer to prevent water from natural sources flooding a quarry and causing problems?
2) Does stationary water have the same impact, say, if I mined a 64x64 quarry then filled it to the top of stationary water? (NOT flowing water).