Unity Android app crashes when launched from Facebook Messenger app.

I am converting an existing Unity Android project (Unity 4.6.5, if that matters) to work as a Facebook Messenger plugin. Part of this process involves allowing the user to launch the Unity app from within the Facebook Messenger app. After implementing the Facebook Messenger SDK this works, provided the Unity app isn't already open. If the Unity app is already open, it will crash.

Searching around the web for similar issues has raised some suggestions, none of which have fixed this problem. I have tried changing the "clearTaskOnLaunch" flag in the manifest, which had no effect. I've also tried changing the launch mode of the activity in the manifest, only to discover that this is then overwritten during the Unity build process. I then tried changing the manifest in a post-build step as suggested in this thread, but found no real information on how to do this on Windows. Finally I tried building an Android Studio project and changing the manifest there before compiling but ran into problems trying to actually compile the project.

My question then is does anyone have other suggestions for what could be causing this problem? Or a link to a comprehensive guide on modifying the manifest that Unity produces (whether through a post-build step or Android Studio/Eclipse)? I would very much appreciate any help with this issue.