I think I can probably venture a guess. My company, and several others in my industry have started using the "Good" app to make Iphones and Androids act like blackberries. Providing access on the devices to corporate email, contacts, and calendar. Since this information is confidential, the application is being set to check for Jailbroken Iphones or Rooted Androids. If the device is rooted, the application locks the account.
To be honest, I have no idea how the application looks for "rooted" devices. If I could figure that one out, I would try to fix that.
I had my account locked out of my company, but would rather have a rooted device than the convience of email/calendar. So now I carry around an incredible and a blackeberry.