When installing Lync the other day I came across an issue where certain users could not view presence status of users in Outlook 2013. When investigating this I found that all users had the exact same version of Office 2013 with the same updates but some users were seeing presence just fine. I concluded that it must be a common issue with the local machines rather than the Lync server so I began to try and find the common link between each affected user. It turned out that the users affected were part of the Cisco Voice team. I also found that each of these users had Cisco Jabber installed, or had been installed at one point.
It turns out that it was a user profile issue where the Cisco Jabber whether it was installed or not had been set as the Default IM App Provider. This is read by Outlook 2013 to determine presence.
In order to resolve this I needed to change this. I found the offending registry key
Change the DefaultIMApp String Value from Cisco Jabber or whatever it is to Lync
Restart Outlook and presence will be shown.
If you have to modify this for a large number of users then perhaps a user logon script to address this would be a better approach
reg delete "HKEY_CURRENT_USER/Software/IM Providers" /v DefaultIMApp
reg add "HEY_CURRENT_USER/Software/IM Providers" /v DefaultIMApp /t Reg_sz /d Lync
Obviously the user executing this script should be able to modify the registry. As it is HKCU there should be no massive issues in doing this