Yeah, i biseced it down to (and reverted)
"ENGR00141363-ARM-imx53-clock-change-di0-clock.patch" from both
freescale's 2.6.35 11.09.01 bsp, which fixes the uart clock
corruption...
I believe I have an identical copy of the Ubuntu kernel booting under u-boot-2011.12. Carefully examining the boot messages coming from Ubuntu with the old u-boot and my kernel with the new u-boot there are some curious device failures. For instance, USB devices aren't being properly initialized and enumerated as well as problems related to the hub. Also, some of the voltage regulation devices are not found.
I'm suspecting that besides the UART timer issues mentioned above that were fixed with the patch, there may be other similar clock related issues lurking in the code. I'm going to modify the new u-boot to report all the clocks so I can do a side by side comparison between the two versions of u-boot. The UART clock issue demonstrates that the kernel code does seem to make some assumptions with regards to the state of the system left behind by the bootloader. Of course the clock settings are just one aspect that could be causing initialization problems, but it's probably a pretty good place to begin looking.
Also, I'll boot my new kernel under the old u-boot just to see if it then begins behaving in an identical manner to the Ubuntu kernel during boot.
Mike