Create a short quicktime video clip that has the same properties as the quicktime video that you want to use in Encore.
Use AE to convert the short clip to the proper framerate and then import it into Encore. Then import the short clip directly into Encore. Make a timeline for each video then burn the project to an RW disc. Play the disc back with a software DVD player and then again with a hardware DVD player. Which file gives you better quality on the finished disc?
If I had to choose blindly, I would change the frame rate in AE.