Can you tell me whats installed, is this a plain jane. I have heard of people having problems if they are running a theme. I am only using the default theme, could this be an issue with you?
stopmaemo should be run as user, the variables in the stopmaemo script are necessary to get matchbox to stop. I only ran as user, no sudo is needed. If you look in the stopmaemo you will see the line to stop matchbox, what happens if you run that manually.
You say you "SEE" matchbox is still running? Are you talking visibly, not ps? You can not see matchbox running, you can see maemo-desktop running?