Looking over this, and what I'm seeing in-game, things like wood carts only accept the specific vanilla blocks allowed in them.
Using the wood cart as an example, it only accepts oak/spruce/birch/jungle, but not acacia/dark oak (Blocks.log2, which didn't exist in 1.6.4), or any other modded logs that register as logWood. Same goes for planks (plankWood), seeds for the grain cart (listAllseed, registered by Pam's Harvestcraft), and various crops (crop*).
Any chance this could be amended?