I've read related questions and still need help. 

The other day, after verifying both "example.com" and "www.example.com" and setting the preferred version as "www.example.com" in Google Webmaster tools, I submitted by sitemap with 139 URL's (sitemap URL above). After the process was complete, only one of the links was indexed, this was the main page "www.example.com".

I am really unsure of why this is, my sitemap is correctly formatted (W3 validated) has the correct URL's, the "www" versions that point to my content.

- I am 301 redirecting all non-www URL's to www (my preferred version)
- After seeing that both "www.example.com" and "www.example.com/index.php" were being indexed (duplicate), I removed the latter through GWT and set up a 301 to redirect the latter to the former to resolve it.

I uploaded the site two days ago (could it be because the site is new?).

I would really appreciate some guidance here as to why this is happening.