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I think the problem here is most likely the Home Customizer. It's designed to look for HTC Home on the Today screen, so, when it reactivates "Home", it does so on the Today screen, causing multiple copies of it to be running simultaneously.

What I would do is first, disable HTC Home on WAD, run the Home Customizer, then after you've applied the settings, reenable HTC Home on WAD. This will simultaneously disable it on the Today screen in an attempt to stabilize the system.