probably just have a diferent nintendont dol version on one of them or diferent settings forced on each.I REALLY like this tool! Though I have had an issue with 007: Agent Under Fire Reloaded.
https://www.romhacking.net/hacks/3731/
It will run fine on my Wii through USB Loader Gx, but as a Wii U channel it will eventually crash on stage 2, though not always at the same point.
I have not tested it under the vWii yet, but wanted to bring it up to see if anyone else has had similar experiences. And to showcase this amazing MOD!