directories with two one dot (.) entries
Yes it's really a duplicate. And a force delete may have worked, but an fsck was the proper fix. Basically, I ran fsck, and it saw some bytes it thought was a directory, so it just put a directory entry for it in the lost+found. Running fsck again actually checked the contents of the directory, found the duplicate, and removed it.
I recommend checking the inode listing of the directory. It's possible that they really aren't the same file.
ls -al -i
You might also check to see if one of the directories has a hidden (or non-printable) character with:
ls -al -Q