In my case, I hit it when I upgraded a site from 1.8 to 1.12.3. In in-between versions I have only updated the Tidypics, as it required upgrade in one version. All other plugins were disabled in 1.8 prior to upgrade and not installed up until 1.12.3. I do not recall having installed CKeditor ever in 1.8, as far as I can tell. It is activated in 1.12.3 though.
In any case, I hit the problem not with CKeditor but with a custom "plugin" of few lines. I thought the issue was something to do with file ownership or access rights of the copied files. But when I simply deleted the db entry it worked. So I have not checked the rest.
Strange... I've upgraded 5 sites from 1.8 -> 1.12 to date and haven't experienced it. That said, I've never used ckeditor in 1.8 which seems like it may or may not be a factor. If anyone has a copy of a db where this is happening I'll take a look.
Thanks Cim @manacim
My problem has been resolved now...
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I managed to fixed this issue, it really was a database issue. I looked up "ckeditor" via phpmyadmin and an entry showed up as "CKeditor." Delete that and the plugin will show up on the list again.
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