Dissolves are one of the hardest things to encode for MPEG-2, so that’s where you’d expect problems.
In Compressor, do you have motion estimation on “Best”? 2-pass VBR?
Beyond that, increasing your peak bitrate will help. Great if you’re getting stamped media, but much higher could cause problems on DVD-R media. If you’re targeting stamped, push up the peak to 9 Mbps.