Please read: http://minecraft.gamepedia.com/Minecart_with_Furnace
and see http://minecraft.gamepedia.com/File:FurnaceMinecartTrain.png
For a long time this is how minecarts with furnace's worked (I am slow to update my server since around 1.4~1.6 due to new release problems).
Now:
The furnace seems to have no affect, the cart looks to move more than an empty cart but will stop after a corner or if it touches another cart. a train no longer works (minecart with chest in front of minecart with furnace, put coal in furnace and watch choo-choo go! )

Its very sad

It was fun to build trains and automated trains with MinecraftFurnace's