We are using SCCM 2012 R2 in conjunction with WSUS to push out Windows Updates to all our client machines. This has worked well for some time with one exception. Once in a while (about every 3 weeks, but not regularly), for no obvious reason, the compliance % on all the deployments for the Update Package shown in the SCCM console resets to 0 and all the machines move from a status of "Compliant" to "Unknown". If we wait, slowly the compliance percentages increase once again. I assume these numbers climb as machines check in again with the primary site. Spot checking indicates that the machines are getting the updates, this appears to be a reporting issue. It is extremely frustrating as it means we cannot rely on the numbers we are getting to from the console reporting which machines have, and which need, the updates. Any ideas why this may be happening, or how we can stop it?
SCCM 2012 R2 (On a Windows 2012 server), Single Primary Site (No Central Site), ~2500 computers located across the US running Windows 7, Server 2008 and 2012.