I just found out what was happening. Encore’s preview is terrible and doesn’t reflect the quality of the streams. I encoded the files using AE and brought them into Encore. Since Encore didn’t need to transcode them, it passed them directly to the disc. The key to this is to encode in something else.
I was used to DVD Studio Pro where it would show you exactly what your streams would look like instead of a proxy. Adobe should give some consideration to fixing this. Would clear up a lot of confusion.
After this experience, I’ll definitely switch to Apple’s solution when it comes out.