the same problem was their with my website & i posted this in the SEO forum.
According to them, google analytics only shows the human clicks means it excludes the search engine spiders hits & visits. Also they track only those pages where u have placed the javascript code. So if any file not having javascript code will not be tracked.
Ur third party software track each & every page clicks whether the page is test page, login page etc.

Also, third party software counts images, flash & other downloads which increases the count. Lastly third party counts urs visit also whereas google analytics doesn’t count the same.

Hope u got ur answer.