After Tuesday August 11, 2015, many users began to report receiving Flash Player alerts or warnings when using Internet Explorer 11 (IE11) on Windows 8.1 or Windows 2012R2. These popups warn about action scripts and other flash features.
The good news is that there is nothing to worry about. Your computer was NOT hacked or infected.
What happened was that in the August 2015 Windows updates, Microsoft accidentally updated the embedded flash player in IE11 with the “debugger” version of flash player instead of the normal version.
Microsoft has updated the notes for KB3087916 to reflect this known issue, which Microsoft says should be fixed by August 18th.