Like with the resolved TNT Minecart bug, ordinary minecarts will disappear after quitting and restarting the game. My personal experience with this has been as follows:
1.) Ride minecart in rail to location. Park it on inactive power rail.
2.) Eventually save/quit at some point
3.) Start the game at another time
4.) Minecart is completely gone and despawned.
Some minecarts do this, others do not. Personally, this has all happened to me in the Nether, but all of my rail systems are in the Nether, so it's not a good assumption to make.
The despawning can happen regardless of when I restart the game after I quit it. I've had it happen after restarting the game a day after quitting it and (just now) after saving/quitting my world, going back to the main menu, and reloading the world.
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Valiant, that's MC-65040
This may still be occurring in 1.8.1. There was a mine cart with hopper running back and forth on rails supplying my furnace system with coal. When I returned to my workshop after a long journey, the mine cart had disappeared.