Scott,

The air flap is a possibility, but it really sounds like a small vacuum
leak.  As the engine heats up, the rubber expands and somewhere is
causing you a slight leak.  Look at all your lines and replace if
questionable (EXTREMELY cheap!).  These lines may LOOK okay, but can
have enlarged over the years to where they can cause a slight leak at
the connection points.  Also look at the air intake boot at it's
connection to the air flow meter.  

At speed, you don't see the effects because the O2 sensor is reading the
extra oxygen and compensating for it.  Vacuum leaks make themselves
known primarily at low speeds or at take-off (not at idle).  A more
severe leak will cause it to kill at take off (lots of fun at redlights
& stopsigns!)

Hope this helps!
Tonya
87 Vanagon GL Wolfs
74 S. Beetle