Bob,

Welcome to the FOG.

You might want to check out Rick's supplemental manual for the domino - it shows how to calibrate/adjust the domino to avoid this. My domino is slightly out, too, but I haven't gotten around to following Rick's instructions yet. This has, however, reminded me that I need to get it done...

I'll post back when I find the link.

No offense intended but I have to ask...
Are you referencing off the same face for the boards you are joining? (don't try to use the height measurements for more than general ballpark estimates)
Is the base of the Domino machine suspended in air when you plunge your mortise?  (If the boards are thinner than ~3/4"and not elevated, the base hits the workbench and throws your registration off)
How many seconds does it take you to cut a Domino mortise? (Fast plunges can throw your registration off...I try to count to 4)
Where do you hold the Domino when plunging? (I am less likely to lift the reference plate off the board if I plunge with just my fingertips back at the Plugit adapter)

What I would do:
Glue dominos into the mortises you have machined.
Practice on some scrap of the same stock while the glue dries.
Get a Flush Cut handsaw and flush cut them when dry. 
Do over.
That's one of the joys of a Domino.  It hides practice.

You don't say clearly what direction the boards are misaligned  .

If you are getting a step in the face surface, the most likely explanation as already mentioned is that you are referencing the domino fence on opposite faces of adjacent boards when cutting the mortises.  The best way to avoid this is to lay the boards out as you plan to join them and then marking all of the visible surfaces.  As you mill the domino mortises, make sure you can always see the marks, i.e. the boards are kept same side up.  It's also possible that the fence height is slipping, though the systematic difference of 1 mm makes that less likely.

If the ends of the boards form a stair step, you are having a problem with horizontal alignment.  If you are referencing from pencil marks using the plastic gauge, your gauge is misaligned.  If you are spacing by putting the fence pin into the previous hole, you need to adjust the movable pin.  Rick Christopherson's manuals, cited above, have directions for making both of these adjustments, or you could send it back to Festool for tuning.  I usually leave some extra length in boards for a table top and then trim them after assembly, so this direction of alignment isn't a problem for me.

Steve