You should have upgraded eem first - can you give a summary of how you upgraded your clients?
Our EEM version reads 220.127.116.11
on the clients - 5.2.9 was the existing client. From there we ran a install of 5.2.12. It seemed to upgrade with no issues until it sync's on the desktop.
Yes, that's to be expected then - you can't upgrade by installing a new version manually, you upgrade by modifying the settings within eem itself, then the clients download the new files and upgrade themselves.
There is a chapter on upgrade within the eepc admin guide - that explains how to upgrade properly.