If it put your mind at rest, I had the same problem on a SIN to NRT.
The payment was not processed but the seat allocation remained.
I checked in online and my seat allocation was not changed.
At the airport I was given the boarding pass with the correct seat number, so despite the inability to pay, it all went as planned.

I guess of all the features that are still not working on the new website, this preferred paying seat function is not top of the list of things they need to fix.
One of my colleagues tried to book a ticket using Safari on his ipad.
After several attempt, he kept getting the same error message 'departure point invalid'... guess what, the departure point was Singapore... So I guess the preferred seat is a small problem compare to not being able to buy ticket out of Singapore on a Singapore based airline!