Adsense will only count impression's for those it will show. I get around 5k~15k total ad unit impression's a day, but adsense only counts around 500~2k of those advertisments.
On your Reports page, Show data by switch it to ad unit and it should show you the number of ad units shown on your pages. The default is to show you the page number that adsense has shown advertisments on.
For instance I have shown 2,592 advertisments on my site and adsense reports me showing 800.
Anyhow, setup advertisments to show in the PSA place aka when google has not advertisments to show. You can link to a .php file and then use that file to include something that will rotate different advertiments and also keep a count of how many times google is not showing advertiments on your site. Keep in mind if you do keep a count it will be ad units and not the default pages like google usually does. Might want to put a check in the php to make sure it was a different page that was loaded when counting it.