I was having a similar issue.. here is what I did to fix it.
First I made sure it could be seen by ADB loop when the phone was not in the bootloader screen. Then I shut it down and reformatted the SDcard in an external card reader.
Open up 2 command prompt windows and start loop in one and have this adb command in another "adb reboot bootloader" but do not hit enter.
Reboot the phone while plugged in to the USB and during the HTC boot screen you should see the phone show up in the loop this is when you hit enter on the adb command it will then reboot the phone to the bootloader screen and follow the instructions from there to flash the rom/root.