I think I got it. Ozone 4 is running in demo mode as a plug-in (because my key is elsewhere), although the plug-in has not been inserted into any signal path. Check this out from the iZotope website:
Trial Limitations
In Trial mode, Ozone 4 will work without restriction for 10 days. After 10 days, Ozone 4 will operate in Demo Mode, and will insert silence at regular intervals.
I assumed that plugins didn't have effect unless invoked.
Twenty minutes later:
Apparently they do.
I renamed the Ozone 4 VST .dll files, restarted Samplitude and tried bouncing the tracks again. The resampling and dithering proceeded just fine and there are no gaps.
Mystery solved.