It's because of your border settings. If you go to the Skin Editor you can see that you have a bottom border of 30px selected. Therefore the size of your project will be enlarged not by 24 px for the playbar but with 30 px due to the border. Captivate also adds 1 px in the width and 1 px extra because you added a border making the final project size 641px x 511 px.
Simply remove the border and you will get the correct size of 640px x 540px
I don't now if this solves your problem, but I had the same one...
You think that the project will export the same size that the created project, but it adds size!
I do like this, when publishing, I choose "export html" in Output options, then, I open the HTML file with notepad, to get the REAL size of the format.
What you said describes the problem. My .swf should be 640 x 504 but comes out 641 x 511. I imported it into dreamweaver to verify.
Exactly, thank you! Now how I selected the border remains a mystery!
I turned off the border and the problem is solved.