I had this problem, every hour it would minimize itself , it was really weird, so that meant that if I started the game at say 1658 the game would minimize itself at 17 o clock ... every hour on the hour.
however I haven;t experianced this problem the last couple of times I played it, as a matter of fact, I don't remember the last time I had this prob.

but to the point , you should check for spy and ad-ware.
that could be a problem, other than that I don't know... update your version of tha game ( if you haven't done this ) to 1.2 maybe that will help