What phranque said. It is expected behavior. The searches are in fact different.
Example.com is much more specific to the domain than example. Compare serps for [webmasterworld] with serps for [webmasterworld.com]
If your domain was keyword.com, it's not unheard of that you might not be #1 on a search for [keyword]... but not being #1 on a search for [keyword.com] would likely indicate a penalty.