I have the same problem with my Internal 1GB on my N800 (file manager hanging, input/output error etc). My External works fine. But I have been using a kernel with 48hz mode.

If you want, I can make a standard kernel that has the debug http://intr.overt.org/2.2008.50-mmc-kernel/ mmc patch that sends messages to dmesg. But I don't know if it will help you any.

BTW If you have Linux on your computer, you won't even need to flash this kernel. Just boot from it and see the debug messages. When you turn off the N800, it will be back to original kernel.