When using the builder's wand to place TileEntity blocks, the NBT data inside is ERASED.
For example: EnderIO painted blocks, Forestry multifarms, vanilla ctrl-picked containers.

I suggest, simulate player clicks in each of the positions of all the blocks to be placed, as a automatic user do.

Placing any blocks with NBT data will erase that data. Also, wand respect looking-at block's metadata on select very weirdly. This is sure critical bug at some point.