diff --git a/bin/pt-table-checksum b/bin/pt-table-checksum
index cd8ffc0e..feb51eef 100755
--- a/bin/pt-table-checksum
+++ b/bin/pt-table-checksum
@@ -5822,7 +5822,6 @@ sub main {
             if ( ($expl->{key} || '') ne $nibble_iter->nibble_index() ) {
                MKDEBUG && _d('Chunk', $args{nibbleno}, 'of table',
                   "$tbl->{db}.$tbl->{tbl} not using chunk index, skipping");
-               $tbl->{nibble_time} = 0;
                return 0;  # next boundary
             }
 
@@ -5835,7 +5834,6 @@ sub main {
                     && $oversize_chunk ) {
                   MKDEBUG && _d('Chunk', $args{nibbleno}, 'of table',
                      "$tbl->{db}.$tbl->{tbl} is too large, skipping");
-                  $tbl->{nibble_time} = 0;
                   return 0;  # next boundary
                }
             }
@@ -5867,12 +5865,18 @@ sub main {
          my $chunk = $nibble_iter->nibble_number();
 
          # Nibble time will be zero if the chunk was skipped.
-         if ( $tbl->{nibble_time} == 0 ) {
+         if ( !defined $tbl->{nibble_time} ) {
             MKDEBUG && _d('Skipping chunk', $chunk);
             $tbl->{checksum_results}->{skipped}++;
             return;
          }
 
+         # Max chunk number that worked.  This may be less than the total
+         # number of chunks if, for example, chunk 16 of 16 times out, but
+         # chunk 15 worked.  The max chunk is used for checking for diffs
+         # on the slaves, in the done callback.
+         $tbl->{max_chunk} = $chunk;
+
          # Fetch the checksum that we just executed from the replicate table.
          $fetch_sth->execute(@{$tbl}{qw(db tbl)}, $chunk);
          my ($crc, $cnt) = $fetch_sth->fetchrow_array();
@@ -5951,14 +5955,14 @@ sub main {
          my (%args) = @_;
          my $tbl         = $args{tbl};
          my $nibble_iter = $args{NibbleIterator};
-         my $max_chunk   = $nibble_iter->nibble_number();
+         my $max_chunk   = $tbl->{max_chunk};
 
          # Don't need to do anything here if we're just --explain'ing.
          return if $o->get('explain');
 
          # Wait for all slaves to run all checksum chunks,
          # then check for differences.
-         if ( $o->get('replicate-check') && scalar @$slaves ) {
+         if ( $max_chunk && $o->get('replicate-check') && scalar @$slaves ) {
             MKDEBUG && _d('Checking slave diffs');
 
             my $check_pr;
@@ -6318,8 +6322,7 @@ sub exec_nibble {
             if ( $o->get('quiet') < 2 ) {
                warn "$error\n";
             }
-            $tbl->{checksum_results}->{errors}++;
-            return 0;  # zero nibble time, skip this nibble
+            return;  # skip this nibble
          }
 
          # This die will be caught by the eval inside the TABLE loop.
diff --git a/t/pt-table-checksum/error_handling.t b/t/pt-table-checksum/error_handling.t
index 50d895d9..88cd61c5 100644
--- a/t/pt-table-checksum/error_handling.t
+++ b/t/pt-table-checksum/error_handling.t
@@ -23,7 +23,7 @@ if ( !$master_dbh ) {
    plan skip_all => 'Cannot connect to sandbox master';
 }
 else {
-   plan tests => 2;
+   plan tests => 6;
 }
 
 # The sandbox servers run with lock_wait_timeout=3 and it's not dynamic
@@ -59,6 +59,57 @@ is(
    "Only one warning for MySQL error 1265"
 );
 
+# ############################################################################
+# Lock wait timeout
+# ############################################################################
+$master_dbh->do('use sakila');
+$master_dbh->do('begin');
+$master_dbh->do('select * from city for update');
+
+$output = output(
+   sub { pt_table_checksum::main(@args, qw(-t sakila.city)) },
+   stderr => 1,
+   trf    => sub { return PerconaTest::normalize_checksum_results(@_) },
+);
+
+like(
+   $output,
+   qr/Lock wait timeout exceeded/,
+   "Catches lock wait timeout"
+);
+
+like(
+   $output,
+   qr/^0 0 0 1 1 sakila.city/m,
+   "Skips chunk that times out"
+);
+
+# Lock wait timeout for sandbox servers is 3s, so sleep 4 then commit
+# to release the lock.  That should allow the checksum query to finish.
+my ($id) = $master_dbh->selectrow_array('select connection_id()');
+system("sleep 4 ; /tmp/12345/use -e 'KILL $id' >/dev/null");
+
+$output = output(
+   sub { pt_table_checksum::main(@args, qw(-t sakila.city)) },
+   stderr => 1,
+   trf    => sub { return PerconaTest::normalize_checksum_results(@_) },
+);
+
+unlike(
+   $output,
+   qr/Lock wait timeout exceeded/,
+   "Lock wait timeout retried"
+);
+
+like(
+   $output,
+   qr/^0 0 600 1 0 sakila.city/m,
+   "Checksum retried after lock wait timeout"
+);
+
+# Reconnect to master since we just killed ourself.
+$master_dbh = $sb->get_dbh_for('master');
+
 # #############################################################################
 # Done.
 # #############################################################################
diff --git a/t/pt-table-checksum/retry_timeouts.t b/t/pt-table-checksum/retry_timeouts.t
deleted file mode 100644
index 11299eab..00000000
--- a/t/pt-table-checksum/retry_timeouts.t
+++ /dev/null
@@ -1,112 +0,0 @@
-#!/usr/bin/env perl
-
-BEGIN {
-   die "The PERCONA_TOOLKIT_BRANCH environment variable is not set.\n"
-      unless $ENV{PERCONA_TOOLKIT_BRANCH} && -d $ENV{PERCONA_TOOLKIT_BRANCH};
-   unshift @INC, "$ENV{PERCONA_TOOLKIT_BRANCH}/lib";
-};
-
-use strict;
-use warnings FATAL => 'all';
-use English qw(-no_match_vars);
-use Test::More;
-
-use PerconaTest;
-use Sandbox;
-require "$trunk/bin/pt-table-checksum";
-
-my $vp  = new VersionParser();
-my $dp  = new DSNParser(opts=>$dsn_opts);
-my $sb  = new Sandbox(basedir => '/tmp', DSNParser => $dp);
-my $dbh = $sb->get_dbh_for('master');
-
-if ( !$dbh ) {
-   plan skip_all => 'Cannot connect to sandbox master';
-}
-else {
-   plan tests => 3;
-}
-
-my $output;
-my $cnf  = '/tmp/12345/my.sandbox.cnf';
-my @args = ('-F', $cnf, 'h=127.1', qw(--replicate test.checksums --create-replicate-table -t sakila.city));
-
-$sb->create_dbs($dbh, ['test']);
-
-$dbh->do('use sakila');
-$dbh->do('begin');
-$dbh->do('select * from city for update');
-
-# city table is now locked until we commit.  The child proc is going
-# to wait 3 seconds for innodb_lock_wait_timeout, then it should try
-# again.  So if we commit at 4 seconds, the child should succeed and
-# the checksum will appear in test.checksums.
-
-my $pid = fork();
-if ( !$pid ) {
-   # child
-   my $output = output(
-      sub { pt_table_checksum::main(@args) },
-      stderr => 1,
-   );
-   exit 0;
-}
-
-sleep 4;
-$dbh->do('commit');
-
-waitpid ($pid, 0);  # reap child
-
-my $row = $dbh->selectrow_hashref('select * from test.checksums');
-ok(
-   $row && $row->{db} eq 'sakila' && $row->{tbl} eq 'city',
-   "Checksum after lock wait timeout"
-);
-
-
-# Repeat the test but this time let the retry fail to see that the
-# failure is captured.
-my $outfile = '/tmp/mk-table-checksum-output.txt';
-diag(`rm -rf $outfile >/dev/null`);
-
-$dbh->do('truncate table test.checksums');
-
-$dbh->do('begin');
-$dbh->do('select * from city for update');
-
-$pid = fork();
-if ( !$pid ) {
-   # child
-   my $output = output(
-      sub { pt_table_checksum::main(@args) },
-      stderr => 1,
-      file   => $outfile,
-   );
-   exit 0;
-}
-
-sleep 8;
-$dbh->do('commit');
-
-waitpid ($pid, 0);  # reap child
-
-$row = $dbh->selectrow_hashref('select * from test.checksums');
-ok(
-   !defined $row,
-   "No checksum due to lock wait timeout"
-);
-
-$output = `cat $outfile`;
-like(
-   $output,
-   qr/Lock wait timeout exceeded/i,
-   "Lock wait timeout exceeded error captured"
-);
-
-diag(`rm -rf $outfile >/dev/null`);
-
-# #############################################################################
-# Done.
-# #############################################################################
-$sb->wipe_clean($dbh);
-exit;