I run a 1.7.2 Minecraft server in Amazon's cloud using Amazon linux version 3.4.68-59.97.amzn1.i686. The server time is set to MST but when the server starts up, logging timestamps appear in UTC. This makes it difficult to correlate events with the logs.

Previous versions have always captured the server time as it's set on the host. When I start a minecraft_server.1.7.2.jar server on OS X, the logging timestamps are correct and match the computer's time. So this appears to be just a problem with Linux, and perhaps only with Amazon Linux.