I'm not sure I understand exactly what the problem is. After the game minimizes itself, does it stay minimized and won't open back up right away, despite the fact that you click on the task bar icon several times, or does it open up and immediately minimize several times?
If it stays minimized, it might just be that your CPU's processing capacity is just maxed out and is working to get caught up. If it keeps minimizing, there might be another application that is active causing it. Either way, this could be solved by closing all unnecessary applications (including explorer windows). One thing I've heard of causing CPU problems is virus software. Check to make sure that this software isn't performing a virus scan at this point in time and either allow it to finish or wait until it's done before playing. Another solution could be for you to play when your computer is not connected to the internet, so you can safely turn off your virus software completely while playing.