Probably related to it being unloaded/loaded.

Setup where problem occurred: http://imgur.com/IL3XxVR

According to @Forecaster the problem vanished shortly after it appeared.

Perhaps a more detailed description would be of use:

I have a long rail line that I'm constructing, I've gone back and forth a few times to test the signals.

Suddenly I reached a signal crossover where it caught the second cart in my train (which consisted of a locomotive followed by a minecart with me in it, followed by a chest cart). I released the train and backed up and approached it again and it happened again, it hadn't happened with any of the other identical setups I passed on the way there. I notified covert on IRC and kept going with the intention of coming back around to see if it persisted. When doing this I encountered a few more places where this happened. I discussed it for a while with CJ trying to figure out why it was happening.

After a while he left and I restarted minecraft completely and went around my line once more finding that the issue had gone away, at least for now.

I will keep an eye out for it happening again and possibly record it.