That is odd, not sure what's going on there. With mine, I can minimize it and it just goes to the taskbar. It sounds like something may be wrong with the install? I'll only say this because if you went to the HEM forums, I would almost put money on them saying it but, "Have you tried uninstalling and reinstalling?"
I know you just made some changes to your computer or were planning on it(Win7?) so either you just reinstalled it or those changes may have made some problems.