Booking on the trainline itself

Does it matter that I can’t book on the Eurail pass site and therefore can’t see the trips on my pass app? Both times I have booked a night train.

The first from Berlin to Budapest we had to have a seat reservation and booked it through OBB using our pass details. Then the second, from Amsterdam to Zurich, showed it was available and included but wouldn’t let me choose it to make the seat reservation that was recommended - ie my cart was empty. So I have also booked on OBB. Just wondering if it matters that I can’t book them on my pass. Or if I am doing something wrong/not seeing something obvious in the process.

Thanks, any help appreciated!