Anything that already uses a display list to render (like the ghost blocks of a patterned template carriage) will not properly render in-transit.

Transparent blocks (like water) render in a bit of a wonky fashion in-transit.

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Portal spawners from iChun's "Portal Gun" mod do not yet work on carriages. Try finding some way (possibly using additional mods) to activate a portal gun directly instead.

Anything using Forge's "multipart" API (such as the newest ChickenBones wireless redstone) do not yet work on carriages.

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If you are using Optifine and get a crash with the word "ConnectedTextures" in it, either disable connected textures in Optifine or disable/remove Optifine.

ComputerCraft programs that are carried by carriages and interact with the carriage's drive, need to have a delay added to their "startup" program to give time for things to settle before trying to interact again. Try "os.sleep(0.1)", and increase that number if it still doesn't work. (The more overloaded your machine or Minecraft is at the time, or the more computers or turtles you have on the same carriage, the higher this number will need to be. Making the number higher than it needs to be is fine: Too much won't hurt, but too little will.)

Computers on carriages that are running at the time of motion will reboot after motion, and run their 'startup' program. (Computers that are off at the time of motion will remain off.)

If a carriage is moving continuously, and the continuous-mode delay is set to 0, tile entities (like chests) will not render properly after the first motion until the carriage stops. This is purely cosmetic, and does no harm. To prevent this, make sure the continuous-mode delay is greater than zero. (The more Minecraft, your system, or the server is overloaded, or the longer delay there is between you and the server, the higher this number will need to be.)