Hmm, I've not had any issues with my (rather older than yours) Vaio Z. Of course, I did a clean install to get rid of the crap (and because the pre-installed Windows 7 was in Japanese) and only used Microsoft Security Essentials. I currently have Windows 8 on it and have no problems there either.
Honestly, from what you're saying here I think the problem is more with Kaspersky than with the Vaio. Also, rather than the "holding back a virus" theory, I suspect the uninstaller simply messed up the system. Almost all virus scanners seem to be crap in some way. Windows Defender (and Security Essentials and OneCare before it) is really the only one that never gave me any trouble.