I'm having this problem as well. Bear with me, it is VERY difficult to explain.
What happens is, when you export a video, your cuts will not be timed correctly. You'll see the 1.5 seconds BEFORE the cut and the 1.5 seconds that should be the end of the shot are cut out.
If you were to take a shot of a clock counting down for ten seconds and trim it so that the edit only contained the last five seconds, it would come out differently in the export. Instead of going 5, 4, 3, 2, 1 like you intended, you would see 6, 5, 4, 3, 2 (in the exported file).
It makes editing impossible, because even when you have your canvas correct, the export comes out wrong.
I've also noticed that if I grab the beginning or end of a clip and drag it to shorten or lengthen the duration, it will show the WRONG (not what I intended to edit) part of the clip. Playback and scrolling look like intended.
My sequence preset is the same one I always use, "Apple Intermediate Codec 1920x1080i60." And I transcoded the file with MPEGStreamclip to the same AIC codec I always use. The only major difference is that the original clip came from a cell phone, though I don't see why that should affect it after I've transcoded it...
Help?