Maybe the spacing is off when you posted it here, but blank lines can affect robots.txt files. Try code:
User-agent: *
Disallow: /cgi-bin/
#End Robots#
Also, check for robot blocking meta tags on the individual pages.
You can test to see if Google can access specific pages through GWT > Health > Blocked URLs (should see your robots.txt file contents int he top text area, enter the urls to test in the 2nd text area, then press "Test" at the bottom - test results will appear at the bottom of the page)