I have a Vaio too. If yours is still under warranty you could give Sony a call:
1-877-865-7669. Here's their website for support:
If not still under warranty you could have a computer shop (of course for a fee) to check it-
Or have Sony repair or replace it. They replaced mine but it was still under warranty.
It wasn't the mouse pad in my case; it was the corrupted recovery partition-
I'm not the expert on hardware but you could run Memtest86 to rule out hardware failure-
You said when you use these commands:
It goes back to normal.....but for how long till the mouse pad (click) stops working again?
Also which make and model of the Vaio do you have? The E series or enhanced?
And how old is your Vaio?