I don't know if it will solve your problem or not, but for the type of thing you're doing I would think a 'while' would be more appropriate. I tend to think of 'for' loops as being more deterministic, and your situation is more open ended. So maybe something like:

while(1)
  { 
  begining:
    print "A\n";
    while (my $job = read_dir("G:/Input"))
      {
       print "B\n";
       next unless $job =~ /(.{1,36})\.txt$/;
       
       my $tag = $1;

       ##'when you have checked all the files' GOTO beginning

       while (my $job = read_dir(G:/Output"))
     {
         print "D\n";
[download]

I'm interested to hear from some other monks.