Mainly for things that have models (such as pneumatic tubes, gates and wires); no idea why o.O

That's really weird... Items should only render like that when they don't know what type of multipart they are... IronChests probably doesn't sync item NBT for the items that get rendered there and that's probably why that's happening. I'll take a look at it and if I can't figure out why I'll talk to CPW to see if he knows what the problem is.

I had a chat with cpw, who told that at the time it wasn't necessary for 99% of the times to sync NBT to be able to display the right item. He also told me that he'd probably change that now, because nowadays more and more items rely on NBT. As he doesn't maintain the project anymore you shouldn't expect any changes from his part though. I've given progwml6 (the current maintainer) a small nudge about it.