I have the same problem (mpeg2 from Compressor into DVDA) but have found a solution… Prepare the project as before, when it fails, go to the prepared project folder. You’ll see two folders, VIDEO_TS and AUDIO_TS. Go into the video folder, find the largest .vob file. This is your main encoded video. In DVD architect delete your previous mpeg2 file, replace it with this one (or start again using this as your video file).
It now prepares properly! Hope it works for you.