I too have a problem with handwriting recognition using the basic S-pen, although the pen works fine for selecting items on the screen. An example of the issue is trying to enter a T but getting only I with no crossbar at top.
I spoke with a Fold 3 tech who reported that neither she nor anyone on her team had received reports of this issue with Fold S-pen. I guess there may be some issues with the S-pen Pro since she reported that the suggested solution for S-Pen problems was to reset the S-pen Pro. She created a ticket but suggested I might try resetting my Fold 3. I tried resetting but that did not help. I will probably just return the Z fold 3 and continue using my note 9 with cracked screen.