Okay, there is an easy way to fix this. Most applications by default have normal priorities(normal:8) but on other instances some applications may force themselves to stay on top(realtime:24, high:13) which allows them to demand more focus over other applications.
simplest way to fix this is to download process explorer(task manager is garbage, you cannot do anything with it) and right click on java.exe or smartremote32 whichever one is showing more focus, Right click>Set Priority> normal:8
and that should set it as any other application when you minimize it.
