You must have something weird set, I'm unable to reproduce this.
Default settings + Crop to remove the tiny black bars from the Wii not having exactly a 16:9 ratio. Auto resolution selection.
I'm guessing that you set your Wii System Menu Setting to 4:3 in Options/Configuration/Wii. There should be an emulated aspect ratio setting there. The reason why it'd work in Ishiiruka is that it might be missing the functionality to actually use the Wii's configured aspect ratio.
Default settings + Crop to remove the tiny black bars from the Wii not having exactly a 16:9 ratio. Auto resolution selection.
I'm guessing that you set your Wii System Menu Setting to 4:3 in Options/Configuration/Wii. There should be an emulated aspect ratio setting there. The reason why it'd work in Ishiiruka is that it might be missing the functionality to actually use the Wii's configured aspect ratio.