Thanks Stuart.
I found the link with the explanation.
It explains why sometimes it doesn't show (when working mac) and other time it does (windows).

If someone has figured out how to set adobe on windows so its default is not to show the box because it prints, I and Dennis at least would appreciate your sharing.

Erika,

I think if you publish one drawing at a time, you won't get the rectangles. The only problem will then be sheets that have refernces within the sheet, such as a detail bubble in a wall section referring to a detail on the same layout.

For these kind of sheets, if you have adobe acrobat, you can selct the rectangles with mouse drag over the whole sheet, and change their properties all at once to be invisible.