On the face of it all you need is a small adjustment to your sort function:

my %seq = ('1035-2341', '1', '1035-2347', '1', '1035-65', '1', '1035-4
+6', '1');

foreach (sort {length $a <=> length $b || $a cmp $b} keys %seq) {
    print $_, "\n";
}
[download]

Prints:

1035-46
1035-65
1035-2341
1035-2347
[download]