I am running into pixelation during transitions. The video looks like it breaks apart in pxels and then gets back together when it gets past the transitions. Any help on this would be appreciated.
You are possibly rendering at variable bit rate with the average bitrate set too low.
This can be particularly troublesome with codecs like wmv and mpeg-2.
Please share your render bitrate settings and encoder information, along with size limitations (are you rendering for dvd?) and someone will likely be able to help you.
One thing that might help you right away is to use constant bit rate.