Does it happen with 1 pass?
CS 5.5, 64-bit, Windows 7.
The stopping point changes on every try. When I go back to the project in Premiere, it's all in the middle of clips that has no filter on them. The source is mts from AVCHD camera. The output matches the input.
I have not yet tried 1-pass. The project is about 2.5 hours long.
I used to have problem with Encore not able to import 2-pass VBR m4v. But never had a problem exporting video.