The recent changes to the SD/MMC stack broke AT91. It seems like there was an assumption that was bogusly baked into the driver. We had assumed that the only data transfer commands would be 512 bytes.
The problem is that the newer stack does commands that are 16 and 64 bytes long. These aren't really needed for basic support of the stack, but to get things like SDHC and high speed transfers working, they are needed.
I've fixed this, and now things work again. I've also taken this opportunity to do some minor cleanups to the at91 mmc/sd driver.