Generikb put up a video with lots of details about their investigation:
Seemingly, their problems were coming from a combination of Xycraft tanks, chickens in water, long Buildcraft waterproof pipes (the ones carrying biomass at spawn) running into unloaded chunks, and the way ChickenChunks disposes of orphan chunks. After addressing these issues, the server appears to be running very smoothly. Nebris, Mhykol, and Pakratt also had some pretty big contraptions running that were a bit suspicious and may have been contributing to the problem.