qaac64.exe --alac --ignorelength -o atom.alac Mother.flac
According to the documentation:
-i, --ignorelength Assume WAV input and ignore the data chunk length.
So you shouldn't be using that parameter if you're using a FLAC file as the input.
(This would be used when reading from a stream where the length of the input data isn't known before the encoding begins)
The online examples also have the output file last.
Try:
qaac64.exe --alac Mother.flac -o atom.alac
-- EDIT --
Replied before I saw you got it working in your most recent post.
The above would be for command-line conversions only - the parameters you need to make it work in MusicBee may be different.
Bee excellent to each other...