I have a hopper minecart on a track that runs for weeks, then suddenly stops as if there is a block in its path. The hopper minecart cannot be found, and when another is placed the behavior observed in the video occurs. When I quit the game (this game is open to lan), and restart (sometimes after several quits and restarts), the hopper minecart will reappear but not in the block area where the problem occurred.

After re-entering the game after filming the video below, the missing hopper minecart was sitting on the track left and behind of the section I displayed in the video, and I could again send a hopper minecart through that space.

This has happened three times on different tracks and I do not know how to reliably reproduce the effect, but I have loaded a video of the glitch, and what I did to try to bypass along with the region file.

http://racinante.com/Minecraft/MC%20Glitch1.mp4
http://racinante.com/Minecraft/r.-1.0.mca
http://racinante.com/Minecraft/level.dat