UPDATE:
Just got off the phone with Nintendo. There is a fix:
In Wii U system settings, you must change your output resolution to 480p before launching Virtual Console. Do this and everything is good to go. You'll have to change it back to 1080p when you want to play Wii U games but this is the remedy for now.
Person I spoke to said Nintendo is aware and there is a fix in the works for this.