It looks like your metadata has changed at some point in the past, probably has been broken for a long time but you've just not noticed. This usually happens if the meta files are forgotten during version control / sharing the project.
Before trying anything MAKE SURE you have a backup.
The easiest way to do this is -
1. Delete the TK2DROOT folder, import the new one.
2. If its just your folders that are broken this will work.
If that has broken your scenes - it means more meta data is broken, and you'll have to update manually. Import tk2d into a brand new unity project, and then copy the files over from the new project into your existing one. Be sure NOT to copy the meta files if they already exist but copy everything that doesn't exist in your current project.