Thanks to everyone who has offered suggestions/possible solutions. To date, none of them have worked and after a group meeting yesterday I found out the problem is worse than I originally thought. For some authors, not only does AE 5.4 not release the folder, but it also ties up the document, causing the entire CMS checkin to fail (the CMS checkin deletes all files in the checkout folder and then the checkout folder itself). This is happening even with multiple documents open in which AE's focus is switched to another document prior to the checkin. This happens for some authors consistently. Others, including me, cannot reproduce the problem in which the closed file is not deleted.
I've opened a call with PTC concerning this issue, C7765517.