Wheakoonga82
Do the affected routes happen to be on ‘panoramic’ PE trains?
If so, try booking the seats on the website of the respective railway operator.
SBB does not operate any PE trains, and the possibility to book seat reservations on trains from other operators has been added only recently to the SBB Mobile app and the sbb.ch website. Therefore that feature might not be always working perfectly yet.
Or the seats might be actually already sold out as we are in the peak season right now. But don’t worry too much in that case, as most PE trains also feature carriages without any reserved seats (check with the railway operator).