So over the weekend I had a chance to upgrade some lab and demo systems to Skype for Business Server 2015 CU3 KB3061064
Installing Skype for Business Server 2015 CU3 KB3061064
First according to KB article, https://support.microsoft.com/en-gb/kb/3061064, it says
Note Updates for Skype for Business Server 2015 will no longer be auto-installed by Microsoft Update. You must manually download SkypeServerUpdateInstaller.exe from Microsoft Update, and then use the following installation steps.
So when you run Windows Update, you do not see the update. Fine no worries, off I download the 90mb or so file, stopped the services using PowerShell (and following the guide above) update applied and updated the databases. This was on both Standard Edition platforms. One of my labs has en Edge server so did the the exact same.
Now here is the interesting bit, I ran Windows Update after the applying CU3 and then it appears in the items to install. I thought it was odd, so ran the update, it first complains that the services are not stopped, so stopped them and tried again. Windows reported that all installed so, green ticks to all items. On the second server upgrade I did, I left the services stopped and ran Windows Update to clear out the upgrade required. I like to have all updates done and not hanging around.