Testflight issue: can only install app on devices that were plugged in directly

We uploaded a new version of our application to itunes connect, and we sent it to the internal testers. However, only those where we installed some version of the application directly through XCode at some point are the ones who can install it via testflight.

Our devices where the app has never been directly installed through XCode cannot install the game right now through testflight (the download gets to around 98% and the says that it was unable to install, even if they had downloaded a previous version of the application through Testflight successfully at some point).

We're using Unity 4.6.2 (we can't update to Unity 5 due to some 3rd party libraries we have not being compatible). Now, this issue started happening after we had to update our project to be used on 64 bit architecture (which required us to change some settings, such as Scripting Backend into IL2CPP and in XCode settings, editing the scheme and putting Release as the build configuration).

So, I'm assuming, maybe there's something in some XCode setting somewhere that could be causing this issue? It seems like something quite specific.