On 21 January 2016, Apple pushed out a silent update to XProtect, its anti-malware protection software built into El Capitan (at least). The new version is designated 18.104.22.168.1.1452910146.
As far as I can see, this only adds Microsoft Silverlight versions prior to 5.1.41212.0 to the OS X blacklist. If your copy of Silverlight has stopped working following this update, then you need to update to the current release. It does not change minimum acceptable versions of Adobe Flash or Java.