Could it be (just a thought) that those users who are not showing up have JavaScript turned off on their browsers?

Google will not track visitors who block or have turned off JavaScript. This also can occur for some users that are behind firewalls.

Since Google runs on JS, it will miss those visits.

Here is a link to the Google help center for troubleshooting tracking issues. It may help.

http://www.google.com/support/analyt....py?topic=7315