Application shows as failed after being patched by WU.

Hi,

I am using SCCM 2012 sp1 cu5 and my clients are running W7 sp1 x64

I have installed Lync 2010 x64 RTM version 4.0.7577.0 to the clients (it also uses a transform to set the lync server name). The installation went fine and sccm client detected the presence of the applicaton (set as by MSI product code and file version number), and it showed as installed in software center and displayed as detected in the appenforce log.

Then I let windows update (from SCCM) patch lync to bring it up to 4.0.7577.4419 and the app upgrades and shows the correct updated version number and everything works. However when the application evaluation scan runs again, it shows the application as failed with a Status of 'Past due - Will be retried' in the software center (i.e. the orig deployment of 4.0.7577.0), and the appenforce log shows as this is not now detected. Which makes sense since it has been upgraded, but is there anyway of telling sccm that it is now an upgraded version so that it will not show as failed, and will stop telling the users that there is a package waiting to be installed?

I did try to add the lync 2010 4419 rollup as a deployment and used the detection as the new MSI product code and file version, and the app had a dependency on the RTM version. This all worked fine and displayed as installed and as detected in appenforce, until the detection process ran again and it then showed as failed in software center and not detected in appenforce log.

Has anyone else seen this strange detection process for lync 2010 x64? Could it be the transform is trying to repair itself, although I can't see that in any of the logs or on the screen.

I've checked and doubled checked that the product code and file versions are correct, and it does say installed and detected on first installation, so I'm not sure of the process to fix this.

Letting windows update patch is the preferred way to go for me, since there will be updates in the future, but how do I stop it from detecting the original deployment now that it is patched and at a higher version?

Thanks

Jaz