I've been troubleshooting for some time on this issue and after being unable to pin this down to a specific mod, I'm coming here for any help/suggestions that can be offered.
In short:
Messages like these (from "latest.log"): [server thread/WARN]: Can't keep up! Did the system time change, or is the server overloaded? Running 2065ms behind, skipping 41 tick(s)
occur about 3 seconds after messages like these (from "fml-server-latest"): [server thread/DEBUG] [FML/]: Gathering id map for writing to world save Answer
which are then very shortly followed by messages like this (also from "fml-server-latest"): [server thread/DEBUG] [FML/]: The world 65ade8e7 (Answer) may have leaked: seen 3955 times.
This, when a player is online, is noticed as as lag in block placement/destruction in most cases, lasting anywhere between 2 to 10 seconds, and can happen every 45 seconds. The tick rate (using server tools TPS command) on the server is generally 12-40ms, except when the spikes occur.
Originally I had thought this to be related to something like forestry butterflies on the server updating leaf blocks and causing many chunks to require disk writes quite often, but recently we've changed the config for forestry to turn off butterfly spawns entirely to dismiss this possibility. Logs are here gist.github - links below. No crashes are caused by this issue, and no memory leaks seem to be occurring that I can detect after letting the server run for a few days continuously.
If there are any ideas what the cause of this could be, or how to continue to troubleshoot this, I'm all ears.
https://gist.github.com/thr33p10/e32035f514dabf9e72b7
https://gist.github.com/thr33p10/e20ece586916dcfd638d