As near as I can tell... since the new update to 8.1 you now have the ability to close your modern ui apps using a traditional "X" on the tooolbar.

The only thing that Modern Mix offers now is the ability to run the modern ui apps in a window.

Running modern apps in a window is the primary purpose of ModernMix.

i don't understand what did this update do because to me it did nothing!!! the windows 8.1 update 1 close and minimize button is still there with "modernmix" and if i close it with the win 8.1 update 1 close button it stays on the background how i know this because i use task manager to see what in the background why stardock didn't fix this issue thats the first thing they should of done and windows mode on modernmix don't even work with win 8.1 update 1 doesn't close the metro apps it stays on the taskbar smh!!.......

Thanks for the good work.

I have two problems with this new version though. First, some apps don't seem to work with ModernMix anymore. The two that I'm having this problem with are 'Nextgen Reader' and 'Mindgames'. They run maximized as if ModernMix is not installed. Clicking the F10 shortcut does nothing and the new overlay is not removed even though I've turned it off in settings. I only tried a handful of apps, so this problem could be present in a lot more than those two. The native windows 8 apps seem to be working just fine though.

The second problem is that when I close an app it stays on the taskbar. If I disable 'show apps on taskbar' from properties, the icons don't show at all anymore. And the 'keep closed application in left hand switcher' is unchecked. This wasn't a problem with the previous version.

Thanks again,

Ditto.

The windowed mode option is automatically added to the 8.1 update 1 titlebar regardless of other settings in ModernMix.

Nope, although I had to just go to confirm it again.  With 8.1 update, you only get close and minimize, along with letting it show it running in the taskbar.  Windowed option only exists when running it with ModernMix.  

Great discussion here: http://winsupersite.com/windows-8/windows-81-update-1-modernmix.  Key quote:

There's just one problem: When you switch to a Modern app from the desktop, it still runs full-screen, and you can't see the taskbar or any other running mobile apps and desktop applications, let alone the Windows desktop. I reported previously, however, that Microsoft will be adding the ability to run Modern mobile apps in windowed mode on the Windows desktop. (See "Threshold" to be Called Windows 9, Ship in April 2015 for more about that important release.) So by the time Windows 9 hits, we should have a more complete integration between the desktop and Modern apps.

However, you may also recall a wonderful little utility from Stardock called ModernMix. (If not, check out two of my posts, Windows 8 Tip: Run Metro Apps in Windows on the Desktop and Windows 8.1 + ModernMix for more information.) That tool lets you run Modern apps in windowed mode on the desktop right now.

With 1.14 beta, the upper windows title bar mentioned in the article disappears - just the windowed option remains.

I think there has been some confusion.

ModernMix adds that option to the 8.1 Update 1 titlebar, but this is always enabled in ModernMix.  There is no setting to disable this so you didn't need to change any ModernMix settings to enable it.  Also the 8.1 Update 1 titlebar when an app is maximized remains enabled with ModernMix installed, again there is no option to remove it.  The only difference is the bar is not shown to you on app open as this was pointless.