There is always a difference in the clicks reported by adwords and the incoming IP's by my hosting stats. They are always less than the clicks reported by adwords, what does this mean, is google checting on us.
May be the tracking script of your host is not good enough :d Why not try google analytics (though i am facing some problem recently)... or someother third party scripts.....
No 2 reporting packages will ever show exactly the same results, as no two are collecting data in exactly the same way.