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Generally I've found unexpected artifacts are **usually** due to something on my system being goofy. The closest example I can recall ATM is before I added another RAM chip and larger HD, I used to get entire 2 or 3 seconds of corrupted video data, like static or misplaced parts of the frames. Re-encoding it with all other applications closed seemed to help, which was my clue.
You can also use the encoder as a standalone without having to open the extremely memory intensive application (Premiere.) The encoder should install as a stand alone when you installed Premiere.