Welcome to Yamaha Synth!

There are only a few things that can go wrong in testing the pedal. Here's your checklist:

_Make sure your FC4 pedal is plugged into the dedicated "Sustain" jack (red arrow below). The way to do this is physically look at the label on the keyboard from the back of the keyboard, because you normally reach over the top of the keyboard it is easier to miss the correct jack than you might think. There are two rows of connection jacks and the most common mistake is plug the pedal physically in the wrong jack... which of course, means it will not work as expected.

_The default setup for the S90 XS's Sustain Pedal is for the "FC3" (continuous) Half Damper Sustain Pedal, so you will need to set the parameter for your FC4
Press [UTILITY]
Select "GENERAL"
Cursor down to find "FS Sustain Pedal" (FootSwitch Sustain Pedal Select)
Set this for your pedal type "FC4/FC5"
Press [STORE] to write your preference to your S90 XS's Flash ROM

In general, Sustain Pedal works on sounds set to receive note-off commands. Ideally test it on an appropriate instrument Voice.
Not much to go wrong in an FC4 (I have one I got in 1983 with my DX7 that still works!) - this does not mean they can't break, anything's possible. But if you discover it is truly not working, return it to your dealer. I'm sure they will be able to test it and/or replace it (since you just bought it) if necessary.

Let us know.