Windows 8.1 Pro x64: Multi monitor taskbar issue auto-hide

Just upgraded to Windows 8.1 Pro from Windows 7 Ultimate.

I'm having a couple of issues with the taskbar, and I was wondering if anyone else has had these issues, and knows how to fix them.

I use multiple monitors, and use multiple taskbars.

First issue: Program on 2nd monitor gets notification, and unhides taskbar (normal). This also seems to unhide my primary monitor's taskbar (not normal).

Second issue: When using auto-hide taskbar, fullscreen videos, such as HTML5/Flash the taskbar is still visible, and the video doesn't go on top. This does not occur when the auto-hide feature is disabled.

For what it's worth my installation is fully updated.

Pictured is an example of the second issue.

Thanks.