After the server was updated to the latest snapshot, it stopped updating logs/latest.log
I honestly have no information what other information I could provide to help with debugging, so I'll just mention that our server is also affected by a "server shuts down when someone enters the nether"-bug
Environment
Debian Linux; java version "1.7.0_25"
OpenJDK Runtime Environment (IcedTea 2.3.10) (7u25-2.3.10-1~deb7u1)
OpenJDK 64-Bit Server VM (build 23.7-b01, mixed mode)
I had this problem. Redownload the jar, it seems to be fixed now.