I am currently having this exact same problem.
My server is running on 3.0.4 (just updated an hour ago to see if it would fix it, it didn't).
i have 24 Gigs of RAM on the server and plenty of spare processor power.
The cobblestone farm was working perfectly fine for a long period of time before I ran off to go find some rubber trees to start a rubber farm. I come back after finishing the farm (mostly) and the cobbles are not forming at all, or at least taking a long long time to do so. The lava is what's taking forever, as water seems to be running in perfect condition.
Oddly enough, if I place lava anywhere else in the server, it seems to flow at it's normal rate, but the moment I put any water in the proper configuration to make a cobble farm, it stops flowing right.
Anyone got any ideas?
