I bought the Wii Amp few weeks ago and faced the same problem : Many files were not recognised on my USB stick.(only few hundreds files were recognised for a total of 5200)
I found out that the problem was related to the file names.
Most of my music files were named like that :
01 - song title 1.flac
02 - song title 2.flac
...
10 - song title 10.flac
11 - song title 11.flac
...
The scan process simply ignores all files with name starting with "0".
This is obviously a bug and my workaround is to remove all "0" at the beginning of all file names.
1 - song title 1.flac
2 - song title 2.flac
...
10 - song title 10.flac
11 - song title 11.flac
With this workaround my 5200 files are all recognized.
Hope this helps,
Greetings from Paris, France
Sébastien