I have reinstalled Knossos as well this time to make sure nothing is installed to Freespace, though there is a library folder in there anyway. Despite setting to what you have, I'm still not getting it to start. Maybe I'm being impatient, but how long does it take to start? I have it installed on an SSD.
Knossos shouldn't take that long to start, probably under a minute.
Unfortunately, Knossos has a known issue
that uninstalling it doesn't remove the Knossos settings, even when you check the "Remove Settings" box. I'm working on fixing this.
Uninstalling won't delete your Knossos library folder, though. I guess we could add an uninstall option to do that, but deleting that folder is a pretty drastic action that we really wouldn't want players to do accidentally.
Are you comfortable deleting the Knossos settings folder yourself?
To do this, first uninstall Knossos.
Then go to Windows's "Run..." dialog by pressing Windows key with R, then type %appdata%
and press Enter.
Then in the Windows Explorer window that pops up, find the folder named "knossos" and either delete it or move it to the Recycle Bin.
At least, this is how to find the folder on Windows 10, but I'm fairly sure it's the same for Windows 7.
Then try installing Knossos again.