You're incrementing $i three times in the line with the split. That makes for many holes in your three arrays. Perhaps a push would be easier. It's a bit longer, though -- I might keep an array of hashes instead.

while (<FILE>)
{
    chomp;
    my ($file, $name, $keyword) = split /:/, $_;
    push @File,     $file;
    push @Name,     $name;
    push @Keywords, $keyword;
}
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