I'm guessing the issue here is how Desktop Manager is installed. If it's installed for BES/Redirector and not configured properly to your email server then it will screw everything up. I suggest you install Desktop Manager for BIS use only and then it won't add any kind of service books on it's own or change any you already have.

As far as the Yahoo app....sorry, have never used it. JiveTalk is my app of choice.