So if I got that right, your problem it's with the System Memory and not the HDD?
I had a problem with an old HDD that was kind of mess up, I could open the system memory and I could move small games (like indies, VC, etc) but when trying to move big games from the System Memory to the HDD (and viceversa) I always got an error and had to restart the system. Also, the games that were on the HDD crashed during loading screens. I just changed the HDD to a new one and haven't had any problems yet, did have to download all games that were on the HDD again though.
Not sure if this will help.
As a general question, can you play games that are on the internal Wii U's memory without problems?
The Club Nintendo page has been down for me ever since they announced the rewards, but today I was finally able to log in and claim the game, so maybe you could try the forums again. If your problem it's with the internal Wii U's memory then you should contact Nintendo asap.
Nintendo and PC gamer
