If you take a minecart from A to B with same height between departure and arrival : no problem.
If you take a minecart from A to B where A is bedrock level and B above ground (example) : no problem.
If you take a minecart from A to B where A is above ground and B is placed deeply enough (difference between blocks) that the drop would kill you : it DOES kill you to exit the minecart.
Death can be avoided by wearing diamond armor + featherfall boots.
Can't be recreated in solo mode, maybe a multiplayer plugin causing this or exclusive to server mode.
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Cannot reproduce.
Can you please zip and attach the world file to this ticket ?
I can't.
The server isn't mine and so i can't access the file.
I'll try to ask the admin to give me the world (since it's a faction pvp server, i doubt it) or at least the group of chunks related to the problem and merge it into another world.
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.

Now please tell me where is the death track ?
I drove from spawn point (some big brick building) several minutes to an underground hub and came out at sign "ascension" - without damage.
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.
This ticket is invalid as it relates to a modded or 3rd party client/server.
Any non-standard client/server build needs to be taken up with the appropriate team, not Mojang.
Any plugin issues need to be addressed to the plugin creator.
This site is for addressing issues related to the base unmodded MineCraft.
May be related to MC-881