Green frames at beginning of clip

I've just pushed out several identical encodes (50+), and just under half of them have exactly 13 frames of green at the front end.

This is just to push out some approval drafts, but will certainly be a bigger issue for the final encode.


Here's the process I'm using:

ORIGINAL:
Canon 5D 1920x1080 H.264

STEP 1:
Trim top and tail in Quicktime 7 Pro (Snow Leopard), save as Reference Movie.

STEP 2:
Episode (5.3.2) strips audio, downscales to 720p pJPG, and adds timecode.

I've been using by-reference movies to avoid encoding twice, but is this an artifact of using by-reference movies rather than originals? Would I be better off converting entirely to pJPG and trimming afterwards?

Thanks in advance,
Rob.

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Freaky People Productions,
Live Event Technical Production
Toronto, CANADA