Hi. Did this ever get resolved?
I have exactly the same problem. I bought an admittedly cheap (£14) unbranded 64GB USB stick (from Zaavi in the UK).
When I got the stick, I plugged it into my PC and loaded some games using Wii Backup Manager. To my delight it worked!
I then added some more games...and it no longer works. Like the original poster, I have tried formatting on the PC, doing it through the Wii Backup Manager program, WBFS manager, you name it. I have tried several different USB loaders on the Wii too. Nothing I do can get it working.
I know everything on the Wii itself is up to date, as I only bought and modded it a few weeks ago.
It still all works with my (unbranded) 32gb stick.
Very frustrating! Does anyone have a solution? Many thanks.