FTF cannot detect if the codec is lossy or not. It can only figure out if it was upscaled from a low-quality version to a higher quality version. So if you convert a 128 kbps mp3 to flac it will be marked as fake.
I have to agree with the previous poster , I converted several 320 MBPS mp3 to wav then to m4a and they all checked out...That is not how this used to work before... I distinctly remember FTF used to id the fakes but now it seems broken..