first of all,if youre doing a factory reset from the phone menu under sd card/storage, or from hboot,with a custom recovery installed,its prolly not really doing anything. those options work with the stock
recovery. in order to wipe your data with clockwork or amon recovery youll go to recovery,and use the "wipe data/factory reset" option.
second: did you complete this whole process? if so, are you s-off? if so,you need to follow the directions in iowas thread to regain root with s-off.
its not a good sign that your usb debugging setting is turning off. does the rest of your data survive a reboot?
if you are still s-on,you can use the htc supertool to gain root access: [UTIL][WIN][01/04] ACS HTC Super Tool v3 - xda-developers
once you get it,id pretty strongly reccomend to follow the rest of the guide and try to achieve s-off.
if youre having some sort of issues,being s-off will make it easier(or even possible
) to fix them.