I just got off the phone with Extensis (Suitcase Fusion 6) tech support. They explained to me that there is a "known issue" with El Capitan that Quark and Extensis know about. This is a known problem AFTER the Quark 2015 v11.2 update.
PROBLEM:
Opening legacy (Quark 10 or earlier) files in Quark 2015 in OX 10.11 El Capitan displays empty text boxes.
Extensis tech support says it is related to the auto font activation feature (plug-in) in Suitcase 6 when used with Quark 2015. Not with other apps, just Quark. He says Quark and Extensis know about this but he does not know who will be addressing it. Quark tech support, if you can find them, know nothing of this issue as I can find.
THE WORK AROUND:
Extensis tech support explained that in Suitcase Fusion 6, under "manage plugins", uncheck the Quark boxes. So Suitcase will no longer 'auto activate' the fonts you are using. So you will need to activate them manually by dragging the font you want to use into the OS X > Library > Fonts Folder. (It will copy it there)
After you quit and relaunch Quark, and open the legacy Quark file, the correct typeface will show up again as expected now.
So it is up to Quark and Extensis to work out a patch. It would be nice of Quark actually let QX 2015 owners know, but I wouldn't hold your breath. I have yet to to receive one single notification from them, despite registering for 'newsletters and communications'.