Never used Procoder 1.x, however, I often see with Procoder 2 that it will misread the framerate, pixel aspect (shows 1:1 when should be 9:10, etc..) and field order (most often shows progressive when it should be lower field) of the QT reference file.
Check your "source" tab in Procoder... The field order is easy enough to fix, just select lower field from the pull down. The PA is easy, click on the "..." box and change the preset to correct. The frame rate is much harder to correct. I've found that the funky frame problem may be caused by using "filler" at the head of your timeline instead of just a blank black title. Often it seems that the only reliable way to get around the framerate misreads is to create a QT using "Same as source" with the Avid DV codec option checked.
Maybe Procoder 3 will address some of these problems...
Just another note...For compatibility I would not create a MPEG2 for DVD with a bitrate over 7000.