Question about Windows 8.1 Multi-monitor

So I updated my desktop PC to Windows 8.1 yesterday. With all of the new enhancements to the Modern UI, I've ditched Start8 and begun using both the Start Screen and Modern UI apps. Below I've embedded an image that shows my two monitors. On the right, my main monitor which has all of my "focus" applications, usually desktop apps (occasionally Netflix or the Windows Store). On the left, my secondary screen which runs Modern UI apps exclusively, with Facebook, Skype and Twitter snapped 95% of the time.

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via i.imgur.com

I do have a problem with this setup, however. Whenever I click a link in Facebook, Twitter or a Skype chat, the links open in Chrome on my main screen, as they should, but the Modern UI apps on my second monitor go into the background and the desktop comes into the foreground when I do this, requiring me to reopen these apps each and every time I click a link. This isn't as big a problem for Skype and Facebook - I don't usually click many links in these apps - but it is a huge problem for Twitter, which I use as a real time news feed.

Is there anyway to prevent the apps from minimizing into the background when I click a link? Perhaps a way to disable desktop mode entirely on my second screen?

Any help would be much appreciated.