Railcraft: 1.10.2-10.0.1
Minecraft: 1.10.2
Forge: 2254

We're skipping to the "steps to reproduce" section

1. Place a vanilla cart on a track.
2. Place a chest in the cart.
3. break the cart with by hand or with a tool.
4. Observe that the chest fall out of the minecrart (we're doing good so far)
5. Pickup cart
6. Observe that the cart is called "Minecrart with Chest" (uhh.. what)
   6 Place the empty minecart on the tracks
7. Observe that the (empty) minecart has a big "Minecart with Chest" nameplate over it.

http://i.imgur.com/eY8LO7A.png

"Place a chest in the cart"
Well, you cannot do this in either vanilla minecraft or Railcraft. This sounds impossible.

hmm ... okay. what's the railcraft way of making a minecrart with a chest? Maybe it's a different mod's bug.

It is to craft a "chest cart" item. You should provide a mod list so we can investigate.

will do. I will also do a little testing to see if there is any more information I can provide

Thats quark... probably best @Vazkii

Modlist: https://minecraft.curseforge.com/projects/unabridged
Will remove quark and see is issue still exists

After removing quark, this is no longer an issue. Sorry for taking up your time.

https://github.com/Vazkii/Quark/blob/master/src/main/java/vazkii/quark/tweaks/feature/MinecartInteraction.java

Railcraft intersects the ItemMinecart usage to replace the vanilla cart with the Railcraft one. If you placed it some other way, it will not get replaced with the Railcraft version. I don't know about the naming though. I don't think that can be Railcraft related since the Railcraft cart never gets placed.

@CovertJaguar Can replacement be done in a way similar to Forge replacing EntityItem with custom item entities?

Not that I'm aware. I used to replace the Item object with my own version but that stopped working in 1.7.