Sharepoint - The file "[file name]" is checked out or locked for editing even though no one has it open
I ended up finding my answer on the Microsoft Support pages. It turns out if the user selected "Edit in [client application name]" to edit the document then after they check it in there is a 10 minute delay before the write lock on the document is released. Below is a link to the support page where I found my answer.
http://support.microsoft.com/kb/899709
You might want to try: From the document library > Settings > Document Library settings > Manage checked out files
In our case, the answer was to clear the Credential Manager entry. Visit the below URL.
http://www.sharepointindepth.com/the-file-is-locked-for-shared-use-by/