Check your Wii U Common Key and make sure you are installing with sig patches enabled.
Most common cause of this error is people pasting in the common key and accidentally including a space.
Are you using 1.0.4 or 1.0.5b? 1.0.5b automatically snips any spaces after the common key, and also checks for the correct common key, in which case your issue would probably be launching WUP Installer GX2 without sig patches.
Fixed, using 1.0.5b now, is this version compatible with .iso too?