I’ve built my game and deployed it as a store app - however the games performance is extremely poor when it’s run as a Windows Store App. If I run it as a normal PC build, it runs perfectly fine on the same machine. It also runs fine in the editor and I’m using a Master build in both instances.
My game is constantly getting above 60FPS on the Windows build so I’m unsure where I should be looking to fix this Windows Store App build?
You could try connecting Unity profiler. Also what Unity version, are you using?
Latest version of unity 4.3.4
I don’t have Pro, I need to be able to use the profiler right?
Does it make any difference if I build a C# project or a C++ project?
In Windows Store Apps, having many rigid bodies and/or particle systems can be an issue. Breaking your scene down into sections and enabling/disabling these as the player enters/exits those sections helps a lot with performance - Especially on lower power tablets etc.
I found that it was due to exceptions being thrown, which for some reason don’t cause an issue on the Windows build but cause a significant issue on the Windows Store Apps build.
For any one else that runs in to this problem, if you run the game in Debug or release mode (from visual studio) and end up with any red writing in a development console, the Master build is going to have significant issues; even if it looks like it works 
My specific issue was this internal unity bug about the tree generator on terrains: http://forum.unity3d.com/threads/210417-project-4-2-to-4-3-Mismatched-serialization-in-the-builtin-class-Mesh/page2
I’ve still got some more issues to work through by the looks of it but resolving those mesh inconsistency has gone a long way to explain the performance difference I was seeing. Wish the behavior was a bit more consistent though