the villager disappears when he's in a minecart
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I've seen this bug as well, and it also affects players.
Steps to reproduce:
Create a long minecart track (around 400 blocks should do).
Put a player or a villager in the minecart and send them off.
Get in a minecart and follow them
The minecart will eventually appear empty. For players, I've seen a stationary ghost of them on the tracks while they are riding. Villagers just become invisible.
When the occupant gets out of the cart, they become visible again.
Note that in both cases they are actually in the cart, it's just a visual bug.
I just tested this again with a longer track (300+ blocks). I still couldn't get it to happen.
This is not limited to villagers, all mobs. Try running a mob in a minecart into a hole with a painting in it. The painting will suspend the minecart, and after a while the mob will disappear, occasionally glitching below the minecart. If one of the mobs does not disappear, it will if I log out then back into the server. I was running 1.4 Pre-release, about to try 1.4.2.
EDIT: Still occurs in 1.4.2. I had to log in/out of the server a few times to make it happen. When the mobs (in my case cows) disappear from the minecart, then appear down below an occasionally "flash" into the minecart for a split second. When you try to attack the cows below nothing happens. Destroying the minecart forces the cow to drop.
I read, on the wiki I think, that villagers will become invisible when taken out of a certain radius of their village in 1.3.2.
Within a certain radius, villagers will try to walk back to their village, but outside of this radius they will wonder randomly. Not 100% sure if this is related though.
Happens in 1.4.2 with Players SSP(open to Lan - does this count as SMP?). Player visually stick at a random position above the track whereas the minecart continues empty. When the player leaves the minecart the avater "zooms" (very fast) from the stuck position to the correct place.
Has been fixed according to:
https://mojang.atlassian.net/browse/MC-251
Can someone close it please?
MC-95 indicates this affects players as well.
I cannot reproduce this in the latest version. I however have been able to find a related bug (MC-39) about mobs vanishing after breaking minecarts.