In the GOP, the Iowa caucus and NH primary often have differing results. In 1980, I think Bush Sr. beat Reagain in Iowa. In 1988, both Dole and Pat Robertson defeated Bush Sr. in Iowa. In 1992, Pat Buchanan defeated Bush Sr. in NH. I think Buchanan finished ahead of Dole in NH in 1996. Then in 2000, McCain defeated Bush Jr. in NH.
So since at least 1980 (not including 1984 and 2004 when I believe the GOP was an incumbent who was unopposed in the primaries), Iowa and NH have always had different results.
So it's not that surprising if there ends up being different winners in Iowa and NH in the 08 primaries.