My best guess would be to upgrade your server to SP4 and see if it helps, or to open a ticket with BMC under your support contract and see if they can get you some troubleshooting steps to try to get this resolved.
we have seen this too on one of our test systems, but not on another one. Not certain yet, but i suspect that the arsystem is crashing at some point and it looks like the armonitor restart doesn't have jetty in the command. So it works fine from a manual restart, but isn't restarting from an armonitor command.
The problem with that thought is that the Jetty server is embedded in the AR Server java process, so it's not possible for it to stay up when the process starts....I'm certainly not on the server team but I'm not familiar with anything that would cause the jetty server to stop responding by a remedy server restart...but logs could show if there was a server restart in the middle of things.