script.pl:

  opendir(DIR, $MyApp::Conf::SUBMITROOT) or die "Can't read dir: $!";
  foreach (grep /^\d+(?:-\d+)?\.\d+$|^[\-\w]+\.\d+(?:\.jpg)?$|^set\.\d
++(?:-\d+)?\.\d+\.jpg$/, readdir DIR) {
    $h = {};
    $h->{File} = $_;
    if (/^(\d+(?:-\d+)?)\.(\d+)$/) {
      ...
    } elsif (/^set\.(\d+(-\d+)?).(\d+)\.jpg$/) { # this is the case we
+'re hitting
      $h->{Set} = $1;
      $h->{Set} .= "-1" unless $2;
      $h->{Timestamp} = $3;
      $h->{Pic} = 1;
      my $curpic = $db->GetSetPictures({SetID => $h->{Set}, PicID => 0
+});
      $h->{New} = not keys %$curpic;
    } else {
      warn "Unknown file: $_";
      next;
    }

----

in the $db object:

sub GetSetPictures {
  my $self = shift;
  my ($param) = @_;

  croak "Bad params" unless exists $param->{SetID};

  $param->{Self} = "/inv/sets/$param->{SetID}" unless exists $param->{
+Self};

  my ($setinfo) = $self->GetSetInfo({Set => $param->{SetID}});

...

sub GetSetInfo {
  my $self = shift;
  my ($param) = @_;

  my %where;
  if (exists $param->{Set}) {
    if ($param->{Set} eq '*') {
     ...
    } else {
      if ($param->{Set} =~ /-\d/) {
        $where{ID} = $param->{Set};  # this is our case in all 3 itera
+tions
      } else {
        ...
      }
    }
  } else {
    ...
  }

  my @res = MyApp::Sets->search_where(%where);  # Class::DBI object wi
+th the AbstractSearch plugin
  ...
[download]

I don't see anything in this code that would explain it. I think you should try putting in some warn statements to show the value of wantarray() inside those subs, and then use the debugger to figure out exactly where that array ref changes.