Ops I misread you talk about countdown on multiboot menu and not countdown on u-boot menu.

N900 has some hardware watchdog.
If software not reset some Hw register every x seconds, N900 will be rebooted (or powered off).
This prevents software stalls, if Maemo hangs then it stops to reset the watchdog register and so watchdog will reboot N900 to exit the blocked state.

Watchdog timers are near 30 sec.

Multiboot during boot process loads a watchdog handler to avoid watchdog reboots, but in your phone this process seems to fail.