iPod Skipping Since iOS4?

Hey Everyone,
Since upgrading my iPhone 3GS 32 GB to iOS4 and 4.1 I have experienced a weird issue. I have a Pioneer head unit in my car and it connects the iPhone through USB to control it on the screen/listen to music. I have noticed that since upgrading to iOS4 that when I am listening to the music this way its as if I am listening to a scratched CD every now and then. It's like the music skips/jumps a bit. However, when connecting through AUX it does not do this, nor does it when using it in my old FM Transmitter that connected by the dock connector.

Has anyone else heard of such an issue? Is there a way I can fix this?

Thanks for any help.