Hi houston photo, welcome to the forum and the site. Your problem requires a bit of detective work, and to do that we'll need a little more information. Think of it as diagnostics...

Now, these lights are identical, right? That should make things easier. Ditch the light modifiers for now (softboxes), and let's work simply with the lights themselves. The first thing I would do would be to label each light unit, say "A" and "B". This will avoid confusion if there turns out to be a problem with just one of the lights.

If you have a hand held incident flash light meter, that would be best, but if not, point them at a wall or other reference object that will allow you to accurately evaluate their light output.

Oh, before we go to all that trouble, I should ask the obvious: are you allowing both lights to fully recycle before you take each shot? The single biggest cause of uneven light output in these kinds of situations is triggering the flashes before they are fully recharged.

Ok, so what you want to do is put each light through its paces separately. Start with full power, and dial it down through the power percentages. The light meter readings should be in proportion to the power percentage, and each light should give identical output.

Assuming that goes smoothly, next I would create the two-light setup you describe in your post: one light synced, one on the built-in slave. Make "A" your key (synced) and "B" your slave. Make sure the lights are facing your subject symmetrically. Both fully charged, fire, and view the results. Keep doing this, dialing each one down the exact same amount, until you get to the lowest setting. Obviously, the lighting should be equal from both lights for each of these shots.

If not, make a note of the light meter readings of each and save the images for comparison.

Now, here's the important step. SWITCH the lights out, making "B" the synced key, and "A" the slave. Repeat the entire process, and note any similarities or differences of the results.

Get back to us when you've done this. Something may jump out at you, and it might be that one of the lights has a problem with either its recharging or slave unit. If you get identical "bad" (as in uneven light) results when you switch flash unit positon, it could be the wiring in your shooting space.

Good luck...