Turning off cached mode for shared folders has solved this issue for the most part.
File tab -> Account Settings -> Double-click the account name -> More Settings -> Advanced tab -> Clear the check mark from download shared folders.

To do it domain wide follow this article
https://support.microsoft.com/en-us/kb/982697
or In the Group Policy Object Editor or the Group Policy Management Console, under User Configuration, expand Administrative Templates, expand your version of Microsoft Outlook, expand Outlook Options, and then click the Delegates node. Then set "disable shared mail folder caching" to enabled.
But wait thats not all! i thought it wasn't working because it didn't clear the checkbox, turns out you need two GPO edits to achieve this:
https://social.technet.microsoft.com/Forums/en-US/58c1cb60-7097-4d28-9a2d-24aa3d189c4b/gpo-disable-shared-mail-folder-caching-in-outlook-2013-not-working?forum=officesetupdeploy
User Configuration
Administrative Templates
Microsoft Outlook 2013/Account Settings/Exchange/Cached Exchange Mode
Download shared non-mail folders: Disabled
Both must be set. Each one individually does not do the job. Result:

Still not sure if its a bug or not but this work around seems to work for me and my users.