I discovered a little bug in FileMan-2.0.3. User is unable to unset the view hidden files preference. Solved by replacing the following line in Commands.pm:
my $hidden_file = $self->{cgi}->{hidden_file};
change this into
my $hidden_file = $self->{cgi}->{hidden_file} || '0';
my $hidden_file = $self->{cgi}->{hidden_file};
change this into
my $hidden_file = $self->{cgi}->{hidden_file} || '0';