Properly count num jobs even for non-initial stage

[nshmyrev]

Since learning rate depends on num_jobs_processed

  ilr=$initial_effective_lrate; flr=$final_effective_lrate; np=$num_splits_processed; nt=$num_splits_to_process;
  this_learning_rate=$(perl -e "print (($x + 1 >= $num_iters ? $flr : $ilr*exp($np*log($flr/$ilr)/$nt))*$this_num_jobs);");

it is important to properly increase num_splits_processed even if some stages are skipped due to --stage parameter.