Easy to see a difference considering that there are almost always imbalances in contested/uncontested House races. Also, some races just have stronger incumbents and/or weaker challengers, which may lead to the party not maximizing their potential in the district.
I'd actually find it surprising if it were to exactly match the presidential margin, but I expect it to strongly correlate. Enough so that you can say that people mostly vote for parties now, not candidates.
Yeah, particularly in 2008, when states like Arkansas, Mississippi, North Dakota, and South Dakota barely produced any Republican House votes and Dems won the House PV in Tennessee and West Virginia, mostly due to non-serious/no challengers in states McCain won handily.