Exporting your timeline as MPEG-2 seems to be frought with problems. You have two choice for encoding with DVD Studio Pro.
1- Drag the .mov file into the DVD SP applicationnand it will encode the audio and video in the background.
2- My prefered way is to make a self contained .mov file and load it into the browser area of Compressor and set the bitrates manually.
There should not be any problem having Compressor encode a self contained .mov file into MPEG-2 and .aiff or ac3 outputs.