Autohotkey is a free program for windows. it will let you remap the keys so that when you press the command key on your mac running windows, windows registers it as control. Otherwise, I'm pretty sure there's no way to change the windows system shortcuts.
It's funny for me, I instantly adapt to using ctrl or cmd depending on what kind of keyboard i am using. If I'm running windows on my macbook, I keep accidentally hitting cmd instead of ctrl. but if i'm running os x with a windows keyboard plugged in, I always accidentally hit ctrl instead of cmd.😕