The flac files have an ID3v2 tag sticked to them, this is not the official method for tagging but most players will try to fix this by reading the size of the tag and skipping to the 'real' part of the file.
I suggest that you remove those tags using the batch function/remove ID3v2 in tag panel.
I had a look at the file it uses an old non official method for storing cover art. I tried to bring the program up to date after all those years and implemented the current official way to update tags overlooking any old method, other applications support this using their legacy code for that, I will try to find some time and support this also.
I've run into the same problem. Usually when TGF hits me with an invalid file error for FLAC files, I open the folder containing the files and use the dbPowerAmp to strip the tags. Then rescan the folder in TGF and everything is ready to go. As someone pointed out, I think it has to do with invalid tags already present in the files.