mysqld_safe.sh:

  bug #5001, added conditional if to test if port set, then only kill the processes
  for this port, not all processes (in the case of this bug where multiple servers 
  are killed.)
  The change to the 'grep' to make sure mysqld_safe isn't killed was per Serg's
  discovery that mysqld_safe would get killed. 
  In my testing, in killing one of the pids for a running server, the "if test ! -f $pid_file"
  was the case that evaluated as true, so in order to test, I had to comment that block
  out.

scripts/mysqld_safe.sh

@@ -311,6 +311,7 @@ do
   fi
   if test ! -f $pid_file		# This is removed if normal shutdown
   then
+    echo "STOPPING server from pid file $pid_file"
     break
   fi
 
@@ -321,12 +322,24 @@ do
     # but should work for the rest of the servers.
     # The only thing is ps x => redhat 5 gives warnings when using ps -x.
     # kill -9 is used or the process won't react on the kill.
+    if test -n "$mysql_tcp_port"
+    then
+      numofproces=`ps xa | grep -v "grep" | grep $ledir/$MYSQLD| grep -c "port=$mysql_tcp_port"`
+    else
       numofproces=`ps xa | grep -v "grep" | grep -c $ledir/$MYSQLD`
+    fi
+
     echo -e "\nNumber of processes running now: $numofproces" | tee -a $err_log
     I=1
     while test "$I" -le "$numofproces"
     do 
-      PROC=`ps xa | grep $ledir/$MYSQLD | grep -v "grep" | sed -n '$p'` 
+      if test -n "$mysql_tcp_port"
+      then
+        PROC=`ps xa | grep "$ledir/$MYSQLD\>" | grep -v "grep" | grep "port=$mysql_tcp_port" | sed -n '$p'` 
+      else
+        PROC=`ps xa | grep "$ledir/$MYSQLD\>" | grep -v "grep" | sed -n '$p'` 
+      fi
+
 	for T in $PROC
 	do
 	  break