I was struggling with this issue while trying to install several ROMs. The reason I was getting this is because I was starting with a GPE phone and was trying to install ROMs that we based on HTC's Sense build (Viper, ARHD, etc...)
The reason is that the partition sizes are different between GPE and stock HTC. I believe that you will encounter the same issue if you installed the GPE RUU on your phone and are trying to revert.
I followed the instructions found here: http://forum.xda-developers.com/show....php?t=2733523 which required me to flash the firmware from what I had back to an HTC version (after this step I got the HTC logo upon restart instead of the google logo) Flashing this firmware must set the partition sizes to the appropriate values because after this I was able to install the Viper ROM without issue.
I had this same issue and here is what i did.
Boot into CWM
wipe as usual
->Mounts and Storage->format system ->format Data ->Format Cache
->install zip ->your rom
Worked for me. Thank me if it helps