Ok, Utnik pointed me in the right direction...it's the three imported SVG diagrams on page 18-19 that are causing this behavior. If I delete them all the transparency groups (from all pages!) are gone.
The diagrams are created in LibreOffice Calc, copy and pasted into LibreOffice Draw, saved as SVGs and then imported as vector illustrations into Scribus.
Even if they are in some way corrupt, they shouldn't create these kinds of "errors", should they? Should I post this as a Scribus bug report?