Thumbs up sixaxsis troubles

hi I'm new to the forum I just have a question about this application I have a samsung galaxy s2 rooted with the stock ROM, I have it all syncd up, and it is working.. the problem I have everytime I run it with an application it acts as home keys. I reconfigure and remap the buttons with in the PlayStation emulator I I am using. But still when I press any buttons on the ps3 controller its still acts as home keys.. what I mean is if I press X or star or any other button besides directional it acts as I press the HOME key on my phone but then if I use the directionals it highlights the icons on my phone. So I know it's working how do I get it to work with just the application. Sorry if this sounds really confusing trust me it is is odd