I am using indesign cs5 and got a strange issuse like this.
in the indesign file, i have the page like this with two boxes. which is visible in the indesign file and in the preview also. but when it is exported for pdf, the second box with just stroke is not visible in pdf.
The above pdf opened in Adobe acrobat 8, did not show up the bottom green box in which is in the indesign.
I have checked all the menus and all the options but not found what is the problem.
(Notes: But it shows in the pdf when the pdf done by print>pdf, and when printed also it is visible. When this page is exported to pdf, the box is not visible)
Are you patched to 7.0.4?
Does the green box show if you go to Preview mode in ID?