I apologize if this has been covered before....but I could not find the answer to this question. I am running v.1.5.8

After installing USU several weeks back (and using the included .htaccess file) Google is not indexing over 2800 pages on my site (most of my site). The reason from Google is "Alternate Page With Proper Canonical Tag" is the reason given.

In Admin I have set Enable Alternate URL's to True and set Enable Automatic Redirects to True which should set the 301 redirects. Can someone shed some light on why Google is not indexing???

Thanks in advance for your help,

Jeff