I don't know if this has anything to do with your problem, but on my Pogo E02, which was built initially from a very old version of squeeze, I had to run the command "flash-kernel" after an "apt-get upgrade" in order to permit a new kernel download to take effect. If I didn't do this, it just booted on the old kernel and sometimes complained about bad modules which were no longer compatible with that kernel. If I were not running on NAND, it did not "flash" anything -- it just built a new uInitrd and uImage. You might give that a try.
(I find no longer have to do this once I upgraded to wheezy.)
(I find no longer have to do this once I upgraded to wheezy.)