My issues are not related to having Kaspersky build a datastore, I should have been a touch more clear with my setup. This box has had Kaspersky installed for roughly 2 weeks now, I am still trying to find a way to defrag it.
I noticed that I had long startup times and that the auto diskeeper reports were looking a touch funny stating that pretty much every file on my HDD that was fragmented couldn't be defragged, this is indicative of disk errors. When I ran a chkdisk util from WinPE it started yelling it couldn't fix the errors.
So my journey began trying to narrow down the culprit. I reverted back to a fresh image and re-installed everything slowly. The corrupt/fragmented files didn't show back up until a scheduled KIS scan had happened during the night. Also, I only have KIS scan the C drive and oddly enough it is the only partition on the drive that has these issues