Once again,: not sure about uboot1.3, but it should behave (almost) same way as palis.
Yes, when you boot into multiboot (kb open), then it will check kernel version against selected (in your case: one and only) version and if they differ will flash the kernel. Then uboot is gone.

About your latest problem: .
run noloboot shuts down device? Maybe /sbin/preinit is still from multiboot?
How do you boot to Maemo at all now?

But as this goes totally OT here, please open a new thread or post to the multiboot/uboot thread (post or PM link).