I finally figured out that the visibility of certain characters [spaces, paragraph end, tabs, etc.] was somehow changing without my input. It seems that it is printing that is doing it. I have them selected to be visible and then I print the document and the check boxes have all been reset. Anyone else having this issue?
EDIT: Confirmed it is printing the document that "unchecks" the boxes.... They are there, print dialog opens, they are gone, print the document, Options->Writer->Formatting aids they are unchecked, check them again, now paragraph ends, etc are visible.