diff --git a/egs/swbd/s5c/local/nnet3/run_ivector_common.sh b/egs/swbd/s5c/local/nnet3/run_ivector_common.sh
index d45095ec85b..e0b9af96b8c 100755
--- a/egs/swbd/s5c/local/nnet3/run_ivector_common.sh
+++ b/egs/swbd/s5c/local/nnet3/run_ivector_common.sh
@@ -17,10 +17,12 @@ if [ -e data/rt03 ]; then maybe_rt03=rt03; else maybe_rt03= ; fi
 
 if $speed_perturb; then
   if [ $stage -le 1 ]; then
-    # Although the nnet will be trained by high resolution data, we still have to perturb the normal data to get the alignments
-    # _sp stands for speed-perturbed
+    # Although the nnet will be trained by high resolution data, we still have
+    # to perturb the normal data to get the alignments _sp stands for
+    # speed-perturbed
     echo "$0: preparing directory for speed-perturbed data"
-    utils/data/perturb_data_dir_speed_3way.sh data/${train_set} data/${train_set}_sp
+    utils/data/perturb_data_dir_speed_3way.sh --always-include-prefix true \
+           data/${train_set} data/${train_set}_sp
 
     echo "$0: creating MFCC features for low-resolution speed-perturbed data"
     mfccdir=mfcc_perturbed
diff --git a/egs/wsj/s5/utils/data/perturb_data_dir_speed_3way.sh b/egs/wsj/s5/utils/data/perturb_data_dir_speed_3way.sh
index 048220d62fd..f857ae2bdd7 100755
--- a/egs/wsj/s5/utils/data/perturb_data_dir_speed_3way.sh
+++ b/egs/wsj/s5/utils/data/perturb_data_dir_speed_3way.sh
@@ -1,20 +1,36 @@
 #!/bin/bash
 
-# Copyright 2016  Johns Hopkins University (author: Daniel Povey)
+# Copyright 2016-2018  Johns Hopkins University (author: Daniel Povey)
+#                2018  Hossein Hadian
 
 # Apache 2.0
 
 # This script does the standard 3-way speed perturbing of
 # a data directory (it operates on the wav.scp).
 
+# If you add the option "--always-include-prefix true", it will include the
+# prefix "sp1.0-" for the original un-perturbed data.  This can help resolve
+# problems with sorting.
+# We don't make '--always-include-prefix true' the default  behavior because
+# it can break some older scripts that relied on the original utterance-ids
+# being a subset of the perturbed data's utterance-ids.
+
+always_include_prefix=false
+
 . utils/parse_options.sh
 
 if [ $# != 2 ]; then
   echo "Usage: perturb_data_dir_speed_3way.sh <srcdir> <destdir>"
   echo "Applies standard 3-way speed perturbation using factors of 0.9, 1.0 and 1.1."
   echo "e.g.:"
-  echo " $0 data/train data/train_sp"
+  echo " $0 [options] data/train data/train_sp"
   echo "Note: if <destdir>/feats.scp already exists, this will refuse to run."
+  echo "Options:"
+  echo "    --always-include-prefix [true|false]   # default: false.  If set to true,"
+  echo "                                           # it will add the prefix 'sp1.0-' to"
+  echo "                                           # utterance and speaker-ids for data at"
+  echo "                                           # the original speed.  Can resolve"
+  echo "                                           # issues RE data sorting."
   exit 1
 fi
 
@@ -39,16 +55,25 @@ utils/data/get_utt2dur.sh ${srcdir}
 utils/data/perturb_data_dir_speed.sh 0.9 ${srcdir} ${destdir}_speed0.9 || exit 1
 utils/data/perturb_data_dir_speed.sh 1.1 ${srcdir} ${destdir}_speed1.1 || exit 1
 
-utils/copy_data_dir.sh --spk-prefix sp1.0- --utt-prefix sp1.0- ${srcdir} ${destdir}_speed1.0
-if [ ! -f $srcdir/utt2uniq ]; then
-  cat $srcdir/utt2spk | awk  '{printf("sp1.0-%s %s\n", $1, $1);}' > ${destdir}_speed1.0/utt2uniq
+if $always_include_prefix; then
+  utils/copy_data_dir.sh --spk-prefix sp1.0- --utt-prefix sp1.0- ${srcdir} ${destdir}_speed1.0
+  if [ ! -f $srcdir/utt2uniq ]; then
+    cat $srcdir/utt2spk | awk  '{printf("sp1.0-%s %s\n", $1, $1);}' > ${destdir}_speed1.0/utt2uniq
+  else
+    cat $srcdir/utt2uniq | awk '{printf("sp1.0-%s %s\n", $1, $2);}' > ${destdir}_speed1.0/utt2uniq
+  fi
+  utils/data/combine_data.sh $destdir ${destdir}_speed1.0 ${destdir}_speed0.9 ${destdir}_speed1.1 || exit 1
+
+  rm -r ${destdir}_speed0.9 ${destdir}_speed1.1 ${destdir}_speed1.0
 else
-  cat $srcdir/utt2uniq | awk '{printf("sp1.0-%s %s\n", $1, $2);}' > ${destdir}_speed1.0/utt2uniq
+  utils/data/combine_data.sh $destdir ${srcdir} ${destdir}_speed0.9 ${destdir}_speed1.1 || exit 1
+  rm -r ${destdir}_speed0.9 ${destdir}_speed1.1
 fi
 
-utils/data/combine_data.sh $destdir ${destdir}_speed1.0 ${destdir}_speed0.9 ${destdir}_speed1.1 || exit 1
-
-rm -r ${destdir}_speed0.9 ${destdir}_speed1.1 ${destdir}_speed1.0
-
 echo "$0: generated 3-way speed-perturbed version of data in $srcdir, in $destdir"
-utils/validate_data_dir.sh --no-feats --no-text $destdir
+if ! utils/validate_data_dir.sh --no-feats --no-text $destdir; then
+  echo "$0: Validation failed.  If it is a sorting issue, try the option '--always-include-prefix true'."
+  exit 1
+fi
+
+exit 0