I just downloaded the latest NI updates and it did not know my default VST install locations, in fact "VST" wasn't even selected in the installer. So I suspect this is probably at least partially responsible for why the automatic Service Center install feature screws things up so badly. For the life of me I don't know why the Service Center doesn't let you edit your default install locations - all you can do is select the installer download location.
When I ran the first installer of the updates, it had both my 32-bit and 64-bit locations wrong, so I corrected both. Then when I ran the next installer, it got the 32-bit location right but still had the wrong 64-bit location. It wasn't until the third installer that both install locations were set correctly.