I have no idea if you still need help but I was having the same problem. You WANT to keep quicktime Reference because it is uncompressed. You don’t want to encode it TWICE.
So, I was having the same problem after I encode then I import into Encore and it was doing the same thing. i would have to encode it again. The problem is – at the top where it says formats. Pull down that menu and select mpeg 2 DVD R – The R is the important thing. By default it is just mpeg DVD – you want mpeg DVDR.
Hope this helps.
Todd