I have experienceed this issue a lot. And every time it is a simple solution.. (I hope this works for you!)
Simply soft-reset your Clie and hotsync again by placing the PDA on the cradle and pressing the hotsync button.
Same solution for getting the IR port to work, too...
is it a brand new Sony Clie?
I have a PGE-T615C Earnie Eng
If you are born once, you will die twice.
If you are born twice, you will die once