Is this a plot hole?
So Pepper discovers the video file incriminating Obadiah in Tony's kidnapping/attempted assassination, manages to exit before he can act against her, and grabs Coulson on the way out the door as a human "SHIELD" of sorts.
Then between that time, and when Tony answers an evening call from Pepper in Malibu, Obadiah has the time to visit his lead research scientist, harshly berate him for failing to replicate work Tony accomplished in a cave with spare parts, and then travel to his home, bypass security and have entered like a ninja to stop Tony from learning the truth seconds too late.
Guess the question is, why didn't Pepper, with the resources of SHIELD supporting her, not call Tony within seconds of exiting Obadiah's view? Was she just really upset about not getting her dirty martini, or just a very forgetful assistant?
"I like to watch." Chauncey Gardiner, 'Being There'