diff --git a/bin/pt-stalk b/bin/pt-stalk
index fd80baf5..93c79cc5 100755
--- a/bin/pt-stalk
+++ b/bin/pt-stalk
@@ -862,6 +862,16 @@ collect() {
 
    hostname > "$d/$p-hostname"
 
+   local slept=0
+   while [ -n "$(jobs)" -a $slept -lt $OPT_RUN_TIME ]; do
+      sleep 1
+      slept=$((slept + 1))
+   done
+
+   for pid in $(jobs -p); do
+      kill $pid >/dev/null 2>&1
+   done
+
    for file in "$d/$p-"*; do
       if [ -z "$(grep -v '^TS ' --max-count 1 "$file")" ]; then
          log "Removing empty file $file";
diff --git a/lib/bash/collect.sh b/lib/bash/collect.sh
index 0b7013c8..87a614af 100644
--- a/lib/bash/collect.sh
+++ b/lib/bash/collect.sh
@@ -286,7 +286,19 @@ collect() {
 
    # Remove "empty" files, i.e. ones that are truly empty or
    # just contain timestamp lines.  When a command above fails,
-   # it may leave an empty file.
+   # it may leave an empty file.  But first wait another --run-time
+   # seconds for any slow process to finish:
+   # https://bugs.launchpad.net/percona-toolkit/+bug/1047701
+   local slept=0
+   while [ -n "$(jobs)" -a $slept -lt $OPT_RUN_TIME ]; do
+      sleep 1
+      slept=$((slept + 1))
+   done
+
+   for pid in $(jobs -p); do
+      kill $pid >/dev/null 2>&1
+   done
+
    for file in "$d/$p-"*; do
       # If there's not at least 1 line that's not a TS,
       # then the file is empty.
diff --git a/sandbox/jenkins-test b/sandbox/jenkins-test
index 44266613..7c647749 100755
--- a/sandbox/jenkins-test
+++ b/sandbox/jenkins-test
@@ -59,6 +59,15 @@ export PERCONA_TOOLKIT_SANDBOX="$MYSQL_BASE_DIR"
 export PATH="$PATH:/usr/sbin:$MYSQL_BASE_DIR/bin"
 export LANG="en_US.UTF-8"
 
+# ######################################### #
+# Remove conf files that's shouldn't exist. #
+# ######################################### #
+rm -rf /tmp/pt-*     || true
+rm -rf /tmp/pt_*     || true
+rm -rf /tmp/percona* || true
+rm ~/.pt-*conf*      || true
+rm ~/.my*            || true
+
 #############################
 # Check and start test env. #
 #############################
diff --git a/t/pt-stalk/pt-stalk.t b/t/pt-stalk/pt-stalk.t
index 4c3ead15..ed905eb0 100644
--- a/t/pt-stalk/pt-stalk.t
+++ b/t/pt-stalk/pt-stalk.t
@@ -149,9 +149,9 @@ like(
 # the samples may not be precisely 1 second apart.
 chomp($output = `cat $dest/*-df | grep -c '^TS'`);
 ok(
-   $output >= 1 && $output <= 2,
+   $output >= 1 && $output <= 3,
    "Collect ran for --run-time"
-);
+) or diag("Run time: $output");
 
 ok(
    PerconaTest::not_running("pt-stalk --iterations 1"),