The usual reason widgets don't load is if you move the app that produces the widget to SD, but that's the same for any launcher. So I admit this puzzled me too, since I've never heard of something like this before.
Of course manufacturers sometimes produce widgets that only work with their own launcher, so it's conceivable that if the widget developer and launcher developer are the same they might have produced a widget that only works with their launcher. It would certainly be useful to know what the widgets in question are.
(My homescreens have a mix of calendar, weather, clock, train timetable and music widgets, with no problem. None of these are Nova widgets, and TBH I didn't even know there were such things).