@CapnGoat: Yup, you never had a linkjail folder, true: because you're using Yifan's jailbreak, not mine. Trouble is, it's still installed, but the system seems to be in a slightly (well, more than slightly, actually) broken state, so it's doing stuff wrong.
Restart, and try to uninstall it, then restart again before trying to installing an up to date jailbreak.
And by 'Restart', I do mean a proper full reboot of your device. Unless you messed with your Kindle over SSH, or managed to install two jailbreaks concurrently, that should help clear things up, although it appears to be slightly more dire than that: you should still be able to run custom updates properly.
Last edited by NiLuJe; 10-11-2012 at 06:12 PM.