HD footage. 90 second piece. Imported as Quicktime animation. Exported as Quicktime with JPEG 2000 codec, PNG codec, and a couple of others I tried. Every time, there are large chunks of black in random spots in the footage. Any idea why this might be happening?
A quick check would be to make sure that you have the proper frame rate and also to not have any other programs running in the background to mess with the render. Is your ram preview fine? Go back and check that at the exact times that you get your black footage.
You might want to check your cache. Usually when there is not enough room in the cache it will dump frames in order to make room for the movie to finsh rendering. I know in XP there is a way to get more than 2 gb of ram. http://generalspecialist.com/2006/05/using-more-than-2gb-of-ram-in-after.asp. I recently had a project that had the same problem. However, I am running vista so I couldn't get more than 2gb of ram. Instead I lowered the percentage of the ram cache and memory usage. Go to Edit->Prefrences->Memory and Cache. Try setting the maximum memory usage to 50% and ram cache to 50%. Try rendering that out, it might take a long time to render but it works, unless you got a multi processor or quad. Let me know if it works.