SWF Flash Files Importing into TB w Pegs

Have a problem with my SWF Flash files coming into TB Studio with motion pegs attached, so that when I remove the peg, some of the frames are out of register. Here is my process:

1. Create keys and timing in Studio (no motion pegs - but illustration is moved back from origin in 3D space - if that makes a difference)
2. Export SWF and give to assistant to tween in Flash
3. Assistant imports TB-SWF to stage, performs tweens
4. Assistant exports SWF from Flash, and hands it off to me
5. I import the Flash-SWF into TB and sometimes the resultant layer has a peg, sometimes it doesn’t.

So, what makes TB import the Flash-SWF with a peg, and how can I get it to NOT do that? I don’t see any rhyme or reason for the pegs. I have to edit the frames from the Flash file into existing TB drawing layers, and if the peg is there, I have to move and scale those frames by hand to make sure everything is on register. A pain, to say the least. I could just keep everything as separate layers, but then it gets confusing as to what is what.

Project specs: 24 fps on the twos, all black line art (painting to come later)

Also, when importing the TB SWF into Flash, all the art pieces in the scene are ‘grouped’ individually, based on their TB layers. So, if in TB I have a leaf drawing on one layer, and have the stem drawing on another layer, the SWF imports into Flash as a single layer, but with the leaf ‘grouped’ and the stem in a separate ‘group’. That’s not a problem, but is that normal for how data is passed from one app to another?

Anyway, any help would be appreciated!