For all people have issues with the UARTs on MPC8245/1. In the 2.6.13 kernel we reworked the support for UARTs to be platform devices. If you look at the 2.6.13-rc5 release you will see the changes that went in. Additionally, the sandpoint reference platform code was updated to take advantage of the changes.
Hopefully, these changes will make some of the issues you might be facing less of a problem. - kumar