If this is with the stock Intel HSF, Then I would expect it is not seated properly.
The stock HSF is (1) Famous for not getting the four push pins seated properly, and (2) the Stock HSF is the lowest performance for HSF.
If you plan on keeping this system, Invest $30->$40 for a "GOOD" HSF - The 3rd party HSFs beet the Intel one every way-to-Sunday!
Most commonly recommended, @ $42 Including shipping: http://www.newegg.com/Product/Product.aspx?Item=N82E16835103065
Added - Too much Thermo compound is not good, Thin even coat is good