Probable solution to what's been nagging you
I think the reason that there is confusion about this is on account of the Fly spell description. In the back of some people's minds, this is stuck in.
So to clarify:
1) If you use the FLY spell, you can't run.
2) If you get flight from another means that does not duplicate the FLY spell, you can run, per the monster manual.
Hopefully this will clear up this disagreement.
(Editing note: See the italicized text in the spell description below.)
From the SRD:
Fly
Transmutation
Level: Sor/Wiz 3, Travel 3
Components: V, S, F/DF
Casting Time: 1 action
Range: Touch
Target: Creature touched
Duration: 10 minutes/level
Saving Throw: None
Spell Resistance: Yes (harmless)
The spell’s subject can fly with a speed of 90 feet (60 feet if the creature wears medium or heavy armor). The subject can fly up at half speed and descend at double speed. The flying subject’s maneuverability rating is good. Using the fly spell requires as much concentration as walking, so the subject can attack or cast spells normally. The subject of a fly spell can charge but not run, and it cannot carry aloft more weight than its maximum load (see page 142), plus any armor it wears.
Should the spell duration expire while the subject is still aloft, the magic fails slowly. The subject drops 60 feet per round for 1d6 rounds. If it reaches the ground in that amount of time, it lands safely. If not, it falls the rest of the distance. Since dispelling a spell effectively ends it, the subject also falls in this way if the fly spell is dispelled.
