hi rasinc,
in your crystal reports designer, right click on one of the lines that is not stopping at the proper place and choose Format and then ensure that Extend to Bottom of Section When Printing is not checked on.
also ensure that in Design mode that the lines are not actually extending into the 2nd page footer section.
usually when dealing with lines that extend more than one section it can get a bit painful. it is sometimes best having separate lines, one for each section, and then aligning them.
and since there were many changes leading from cr 8.5 to cr 9.0 there are going to be issues like this, some of them unfortunately leading to tweaking many of your reports.
-jamie