Flash Player Local Storage

So, I have been trying to run this binary java application, and a pop up box comes up for Adobe Flash Player Settings telling me that local is asking to store on my computer. I can get it to click over to the settings using the double finger click with my trackpad (here there is options for settings, and global settings), but then it will not allow me to actually change the setting, or allow or deny it. I have the system preferences for flash player set to allow, and I have gone to the adobe page to mess with the global settings and what not there, but nothing takes. All that happens when running this application is that this pop up box comes up on my screen, and doesn't allow me to do anything. What can I possibly do to fix this? I have tried to go through and clear out any flash remnants, other flash stuff, but I'm not sure if I have actually rid my computer of any and all flash player stuff in order to start over fresh. How do I do this as well? This has been incredibly frustrating. Please help!! Thanks!