Ran into this today as well after trying the Steam version for the first time. It seems like a visual glitch, as challenges I had already completed on Xbox and finished again on PC did not provide any additional Nightwave rep (not that I'd expect them to), but finishing ones I hadn't yet completed managed to sync successfully. The most annoying thing is the "complete 15 missions" tracker reset on both platforms, and now only reflects my PC progress (3, instead of the 9 I had on Xbox originally). I imagine it might still pop after only 6 missions, but not sure yet.