We have 3 multisites
Installed Free Download "Multi Sites Google Analytics" 1.1.0
and using Multisites Version 1.2.95

The code only displays in the header on the sites homepage. If you go to any subpages within the site, the code is missing from the header.

Obviously this does not track the traffic accurally as Google will never see any other pages.

Sample setup
www.domain1.com=UA-12345678-1
www.domain2.com=UA-12345679-1
www.domain3.com=UA-12345671-1

Tracking type Single Domain
Position Head section

Please help. Thank you

I suggest that you also defined the code without the www.

You can also add a default one without any domain - so that you could see which one is taken.

You can also check the html "source page" in your browser to verify that the code is present and based on the GA ID, also verify the domain name that is used by your "sub-pages"

Also ensure that the GA module is present in the slave site