When I tell my N900 to Switch Off! I hear a beep toward the end and I usually have to remove the battery briefly to boot back up. In other words, it looks like I'm not completely shutting down.

This has had no bad consequence, but it makes me wonder.

I looked in the var directory for a log file that might help, but I'm not sure what log file I can check.

I have Bootmenu installed but don't know if that is relevant or related.

Suggestions for how to troubleshoot this?

Have you tried the reboot option instead of shutdown ? Also, do you get any error messages in "dmesg" command ?