Is there something different at the end of the timeline that is not present for the other 99%? Try just rendering the last portion of the timeline and see if the error still comes up.
What HD files are you using? M2T? AVCHD?
You could also try encoding to AVI uncompressed and see if the encode will complete (this way you will get all of the footage up to the point where the error occurred- it is not an all or nothing scenario). If you watched the AVI file and note that all is there, great; encode that to mpeg-2 and see if that will work. Note though, to do uncompressed you will need a lot of hard disk space. You do not necessarily need to use uncompressed, other AVI options should work just fine. Uncompressed ensures you do not lose any quality in the process.
j razz