Multiple users, myself included, have been seeing the same issue on the server that I play on. It's something that's only started occurring within the past week after updating to a newer Bukkit release. Not sure then if it's more of a vanilla bug or something Bukkit has introduced. I was able to upload an example copy of the rail run that I have died multiple times on.
The end-point you are noting is where the death has been occurring, at the "Ascension" sign. I'm assuming this is more likely Bukkit related than a bug in vanilla Minecraft code. I had checked their forums prior and did not see anything noted as far as minecart deaths.