I've been paying bills in CH for nearly eight years now. I've
never in that time paid the bills at the bank or post office. Always online.
So long as the correct reference information is entered, it shouldn't be a problem.
There is a difference between the red/pink slips and the orange slips though. If you've set up a standing order for the orange slips, perhaps you're not using the correct reference number? It might actually change from month to month.
I'd propose to your landlord, that if he wants you to spend time going to the bank to pay these bills, that you'll charge him for your time and inconvenience at 100CHF per hour or part thereof. And that you'll happily accept such payment online, or via the bank or post office as he chooses.