The issue was with an interstitial ad. If you task switch while it was showing, either by tapping the home button or clicking the ad, you couldn't return to the game. I was able to reproduce this in a simple project, outside of any of my code. At the top of the linked post you can find some code to reproduce this in some pastebin links.
The issue seemed to be resolved when setting the LaunchMode to SingleTop through my initial investigation, though I haven't done anything more thorough as I've set aside the ad-enabled feature to focus on the paid release first... I'm kinda wanting to finish this and work on other projects, so going around in circles with the ad stuff was getting tiresome
It was also possible that this presented itself solely on the emulator as I didn't have a physical device at the time, though KakCAT did say that they could reproduce a problem, just a somewhat different one.