If your Vaio came with WinME like mine did, and with the other Sony Custom Software, it is possible to do a "Restore" to an earlier configuration. I've had to do this twice in the last six months and have been well pleased with the result. You don't lose any saved work doing this. (Ah, I see that you have rebuilt Windows anyway so ignore this, but the rest of this post might still help.)
The last time I used "Restore" it was the result of trying to use a McAfee engine update that was incompatible with ME. As a result, I upgraded to McAfee VirusScan Ver 5.21 and it now runs well on ME.
Dont forget the "safe mode" option to check for driver incompatibility. Hope it's not the hardware but it does kinda sound like it! There was a similar problem aired very recently that turned out to be a Cache Memory fault.