Where are .motif files from homer knownResults?
I have provided a solution in Biostars:

If you edit the file findKnownMotifs.pl and move the call to printMotif to come before testing $svgFlag you will find that .motif files are printed again. 

In the following I have commented out the call from where it need not be, and introduced it as the first line, right before the if block:

   printMotif($_, $directory . "/$knownDir/$matrixFile"); # this should be done regardless of $svgFlag                                                                                                        
    if ($svgFlag) {
        my $str = HomerSVGLogo::motif2svg($_,$bitFlag,$rnaFlag2);
            open SVG, "&gt;$directory/$knownDir/$logoFile.svg";
            print SVG $str;
            close SVG;
            print MAIN "$str\n";
    } else {
  #printMotif($_, $directory . "/$knownDir/$matrixFile"); # this should be done regardless of $svgFlag                                                                                               
            `profile2seq.pl "$directory/$knownDir/$matrixFile" 100 &gt; "$tmpFile"`;
            my $width = $widthFactor * $_-&gt;{'len'};
            `seqlogo -a $bits -f "$tmpFile" -F PNG -S -c -o "$directory/$knownDir/$logoFile" -h $height -w $width`;
  `seqlogo -a $bits -f "$tmpFile" -F PDF -S -c -o "$directory/$knownDir/$logoFile" -h $height -w $width 2&gt; /dev/null`;
  print MAIN "&lt;IMG src=\"$knownDir/$logoFile.png\"/&gt;";
}


I expect this change was mistakenly introduced while refactoring the code to support svg as alternate output format for logos.

I have reported this to the author of this code.