I am uploading all of the files now.
The problem looks to be all over the place (randomly).
For example when I click on a help button to display the small help window the link looks like this:
http://forum.domain.tld/admincp/diagnostic.php?do=list#
Should that pound symbol be at the end of the link?
EDIT: All files uploaded, no change.
EDIT 2: When trying to rebuild all languages I see this link:
http://forum.domain.tld/admincp/lang...=language.php? If I remove the trailing "?" the function works perfectly.