If you drop the video that plays well in Media Player on the Vegas timeline, what does your audio look like?
Can you see the stutters?
Do the stutters show up anywhere else?
This might be a youtube problem. You might fix this by adding a second of black with a really low pitch, very low volume hum, so low that it is undetectable. If that stutters no one will hear it.
Just a wild thought.
Jeff
2-Xeon X5680 @ 3.33, EVGA SR-2 Mobo, 48GB DDR3, GTX 580 3072MB, 16TB Attached Storage, Win7, Vegas 11 x64