It is good to know most everything is working for you now ....
As for the minimize problem .... I would assume the problem is due to some spyware software on your computer. I have had this happen to me a couple of times. Does the minimizing of applications just occurs after a game is started or do you notice it with other programs suddenly becoming minimized (ie: email program, web browsers, etc....). I would recommend doing a complete shutdown of your system and then power it on again but do not manually start any programs, just let the computer start all the processes it normal does when you reboot. Then once it is done booting up, do a Ctrl-Alt-Del and select "Task Manager". You then can click the processes tab. Sort the list by the UserName column and then post all processes running under your username. We can then see if there is any spyware running on your machine.
If it is not spyware, then I would assume another program is trying to become active after 1 to 2 minutes .... and when a program is fullscreen (which Mala would be) then it minimizes it. Perhaps an email program is trying to check for email every couple of minutes or something. Perhaps turn off (disable) any virus protection software you might have running and see if that solves the problem.
If all else fails I would recommend starting a new thread in the "Main" BYOAC forum .... not just this "Software" forum. You will most likely get more responses.
Good rule of thumb .... never install anything to the desktop.