Hi, my friends and I keep having the same error on our server. We had no problems until version 1.6 came out. The main problem is when you're breaking a block, it takes a second it to go away and be able to be picked up. There was lag while placing and opening chests, but for some reason it went away after we used Chunkbuster on the server. I really don't know why it worked. However, the block lag still exists! Day and night both have this lag.
Now, if everyone on the server is in the Nether for, I dunno, 10 minutes, the lag goes away completely. There is no lag, whatsoever.
Some other topic with this similar problem says it has to do with the zombie pathfinding (it was changed in 1.6). Other people say it's the server's specs (I don't think that's the problem. The server ran with no problems before 1.6 and no it's acting up...the resources to run Minecraft couldn't have gone up that much). The only thing I know is that no one has a solution and it seems like no one really knows the cause.
We keep getting the same "WARNING! Can't keep up! Did the system time change, or is the server overloaded?" error.
@Zera Fox
We have no plug-ins on the server. There's a lot of caverns below where we made our village and we keep finding zombie spawners everywhere. I've had the same thought as well, but I can't find anything that really makes sense besides the zombies.
It's just really weird that pre-1.6, we were fine, then 1.6 and beyond it's been lagging (which like I said, should point to something to do with the update). Someone noticed something going crazy with our server ticks the other day, too, which should be related to the server calculating heavily. Chunkbuster says there's nothing wrong, as well (I really don't know how it helped the first time, but it did, lol).
If we fix this, I'll post something here and maybe it could help. I dunno.