Logistics. When you have four or five different programs working on footage, sometimes stuff gets confused.
I had to go back and re-render footage in a different format from Combustion. You see, DV footage can be rendered with different flags for widescreen and letterbox, and not every program recognizes both flags. Plus a windows .avi file can have different codecs, so if you render as say an uncompressed avi, it won't necessarily render the same way as the rest of the footage.
This is why we burn test DVDs.
I have three different files rendering right now, and I'm burning both CPUs at 100%. It's pretty cool.