I have Lync 2013 installed on my Windows 7 work machine, which I believe was installed on my machine from day one. A few weeks ago I upgrade the rest of Office to 2013, I believe it was at 2010 before.
It seems that since then I'm no longer archiving my Lync instant message history. I've looked at the Options in Lync and "Save IM conversations in my email Conversation History folder" is unchecked and disabled. In the Windows registry, I've added an IMAutoArchivingPolicy setting under Software/Policies/Microsoft/Communication, it didn't exist before. I've tried having it set to both 0 and 1, but in both cases the "Save IM conversations in my email Conversation History folder" setting remains disabled and unchecked.