23.98 fps video on a DVD will play back as 29.97 fps on systems that don’t support progressive video – the player does the pull-down automatically. And of course it will play back as 23.98 fps progressive on system which support progressive playback.
So if you aren’t already, you should export from Compressor as 23.98 fps MPEG-2 for DVD-Video, and just import that into Encore. Also make sure you are exporting elementary streams, and not a muxed MPEG-2 file.