There's something weird going on with Tyrael, and it may be a hijacking issue like you talked about in the first post, and other subsequent posts in this thread, but I'm not certain because I don't use TeamViewer, or anything like it.
When I start Tyrael and I use the pause combination, it prints in the HB log screen that it's been paused, but the bot keeps going and when I hit the combo again nothing happens. There's nothing being printed in the log screen. I've also noticed that HB has started to have a tendency to hang when restarting, and will go to a (Not Responding) state after a few seconds. I frequently have to close it using the Task Manager. This isn't just with Tyrael, but with anything I do. If it hangs, it won't respond, then I have to end the task.
I have Skype installed, and Ventrillo (though I rarely ever use Vent because there are no raiding groups going on right now), but I do use Skype quite a bit. My PC is always shut down at the end of the day, and turned back on. I've also tried just doing a simple Restart (not shut down and reboot). It still doesn't work. As of right now I have no logs because I'll have to dig for it when I get home to find out which one is the right log. Was hoping for just an "off the top of your head, best guess" type answer.