I have had similar problems with books linked to topics. Have
you tried fixing this in the Generate Printed Doc wizard? The
Content page allows you to make a separate print doc TOC, using the
online TOC as a starting point. Changes to the print doc TOC are
saved in the Printed Doc layout, not the TOC tab.
One gimmick on that page is a check box for Maintain HTML
Levels. If all your topic titles have the same HTML style, this
will iron out the indent differences - but it might do so by
un-indenting everything! ;)
Bottom line - do some experimenting with the Generate wizard.
And good luck!
Elisa