OK...as far as the tool working, there is an issue with the windows version with communication, but that has been partially resolved in the new version (update in OP) and they are aware and still working on solving it entirely. Other than that, there are a LOT of sucess stories coming through in the thread:
http://forum.xda-developers.com/showthread.php?t=725744
I have already rooted, so I haven't tried it myself, but it is working (you will have people not being able to root/flash/jailbreak with any OS/method, but this seems to be getting a lot of easy root stories!!
mbern1008...I am fresh off the WM wagon as well, and know what your going through. I am not 100%, I thought if you did a factory reset you would have stock, but that may have been with the original root method. I will see what I can find out for you.
(chances are they (VZW) won't look for root anyway, but it pays to know for sure)