I don't know if this is the same problem. I installed a new kernel (linux-image-3.1.0-1-amd64) which would not finish booting because the initramfs image was unusable. It turned out that upgrading busybox from 1:1.1.3-3 to 1:1.19.3-4 enabled initramfs-tools to construct a working boot image. Probably initramfs-tools should depend on a later version of busybox than 1:1.01-3.