You must be using gmail in a different manner. I have a domain name along with Google Apps. The Gapps administrator control panel (Dashboard) is where you add/remove users, setup groups and such.
The messages are getting to your phone, so my earlier comment probably is not relevant.
On my phone, Gmail is my personal email and has a small globe in the center of the mail icon. My work one has a briefcase within the icon. Messages is just the mail icon and shows all email, calls,etc.. So, 3 inboxes on my desktop.
Doubt that is any help either, but is it possible that the primary inbox being used is hidden or something?
I'm at a lost otherwise. When I setup the gmail, i just entered my username and password, and started working. I didn't enter server port numbers or any other config info. Google Sync - Google Mobile Help