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wait... on the File > Save As... dialog, does the "*.qtz" appear as an option on the file-type selector?

there should be always one named like "Archive files (*.qtz)"... if there's none then I'm afraid your qtractor build is handicapped, so to speak, probably compiled without libz-dev installed support and that's why you end up with a plain XML file instead of a ZIP one; even though you change the file name extension/suffix explicitly to .qtz, it won't take any effect whatsoever: it will always save as a regular .qtr file but with a misleading extension/suffix though.

hth.
byee