How do I get rid of boxes that appear when I create a pdf from InDesign?

I recently had to install the new Java (jre-8u25-macosx-x64-2.dmg) on my Mac because Indesign would not open.

I am running OS X Yosemite, 10.10.1

Now, when I try to create a PDF from an InDesign file, I get little boxes that appear. I am not sure what to do to get rid of these. When I go back into InDesign, they are not there.

I tried to copy and paste into this message, and they do not show up!

Please Help!