So i ran across this little gem yesterday, and realized this morning what the issue was.
I had some ProRes 422 HQ spots that had been exported from Premiere. Slate up to the first frame of the 2 second mark, black until 1:00:00:00, and then the 30 second spot.
I brought it into smoke only to find that after the slate, there was only a single frame of black, and then the visuals of the spot started the frame after that. The audio was in the correct place, meaning that there was nearly a 2 second sync issue.
The problem? The file had been made with the "Optimize Stills" feature set, which creates a single frame in the video stream of any still and marks it with a length tag... i.e. repeat this frame x number of times. It's the ultimate expression of mpeg-style compression, really. If something doesn't change, don't change it. However, smoke doesn't recognize this extra compression (at least, as of the current smoke 2015 release).
So if you run across this issue, are responsible for exporting media out of an Adobe product, or work with people who use Adobe products in your workflow, it's something to be aware of!
~Scott