Copy all clips and put them in a 1080p timeline.
Make sure Premiere interprete them as prograssive.
Export from Premiere.
If there are any gaps in the video tracks fill them with black video.
Make sure the videotrack has the same length as the audio track.
See if that will help
The clips are already on an 1080p timeline and Premire is interpreting them as progressive. Funny thing is, I tried exporting MPEG-2DVD with CBR instead of VBR and the video length turned out right. Any reason why VBR would cause my video to shorten like this?
Bring the files into Encore and check them. Don't trust what Windows Explorer says about them.
Well, well. It turns out Windows Explorer was wrong. Encore says the m2v file is the correct length. Thanks Jim.