From Premiere, export a short bit (30 seconds) using the same settings you've been using. Do you get the same thing? If so, post the clip (can't do it here) or I'll send you an email address, so I can test it.
I did this, and the new :30 test file worked fine with Encore. I suppose that means there's a glitch of some kind with the original WMV files I was using, correct? (I can't imagine what it was since I used the same settings I always use, but the problem exists nonetheless)