I dont know. All I know is that I wasn't able to replicate it on a Week-old version of the server, and that it was a bug on the online server recently. Today, however, I found that riding in a cart no longer made you short.
My latest modifications to the afk mod made it so that it put players back into the attachment state that the afk mod found the players in. Previously, it would create all sorts of havoc by simply setting an attachment state, as well as an animation, every 5 seconds. That made it impossible to sit on a horse or lie on a bed. While I am not aware of how this may have affected the carts attachments and eye-height, I suppose that it is possible.