diff --git a/src/flow-manager.c b/src/flow-manager.c
index 70300b95cd..56ccce3b24 100644
--- a/src/flow-manager.c
+++ b/src/flow-manager.c
@@ -98,12 +98,12 @@ typedef struct FlowTimeoutCounters_ {
 } FlowTimeoutCounters;
 
 /**
- * \brief Used to kill flow manager thread(s).
+ * \brief Used to disable flow manager thread(s).
  *
  * \todo Kinda hackish since it uses the tv name to identify flow manager
  *       thread.  We need an all weather identification scheme.
  */
-void FlowKillFlowManagerThread(void)
+void FlowDisableFlowManagerThread(void)
 {
     ThreadVars *tv = NULL;
     int cnt = 0;
@@ -121,8 +121,24 @@ void FlowKillFlowManagerThread(void)
     while (tv != NULL) {
         if (strcasecmp(tv->name, "FlowManagerThread") == 0) {
             TmThreadsSetFlag(tv, THV_KILL);
-            TmThreadsSetFlag(tv, THV_DEINIT);
             cnt++;
+
+            /* value in seconds */
+#define THREAD_KILL_MAX_WAIT_TIME 60
+            /* value in microseconds */
+#define WAIT_TIME 100
+
+            double total_wait_time = 0;
+            while (!TmThreadsCheckFlag(tv, THV_RUNNING_DONE)) {
+                usleep(WAIT_TIME);
+                total_wait_time += WAIT_TIME / 1000000.0;
+                if (total_wait_time > THREAD_KILL_MAX_WAIT_TIME) {
+                    SCLogError(SC_ERR_FATAL, "Engine unable to "
+                            "disable detect thread - \"%s\".  "
+                            "Killing engine", tv->name);
+                    exit(EXIT_FAILURE);
+                }
+            }
         }
         tv = tv->next;
     }
@@ -131,24 +147,6 @@ void FlowKillFlowManagerThread(void)
     for (u = 0; u < flowmgr_number; u++)
         SCCtrlCondSignal(&flow_manager_ctrl_cond);
 
-    tv = tv_root[TVT_MGMT];
-    while (tv != NULL) {
-        if (strcasecmp(tv->name, "FlowManagerThread") == 0) {
-            /* be sure it has shut down */
-            while (!TmThreadsCheckFlag(tv, THV_CLOSED)) {
-                usleep(100);
-            }
-        }
-        tv = tv->next;
-    }
-
-
-    /* not possible, unless someone decides to rename FlowManagerThread */
-    if (cnt == 0) {
-        SCMutexUnlock(&tv_root_lock);
-        abort();
-    }
-
     SCMutexUnlock(&tv_root_lock);
 
     /* reset count, so we can kill and respawn (unix socket) */
@@ -913,14 +911,14 @@ void FlowRecyclerThreadSpawn()
 }
 
 /**
- * \brief Used to kill flow recycler thread(s).
+ * \brief Used to disable flow recycler thread(s).
  *
  * \note this should only be called when the flow manager is already gone
  *
  * \todo Kinda hackish since it uses the tv name to identify flow recycler
  *       thread.  We need an all weather identification scheme.
  */
-void FlowKillFlowRecyclerThread(void)
+void FlowDisableFlowRecyclerThread(void)
 {
     ThreadVars *tv = NULL;
     int cnt = 0;
@@ -947,8 +945,24 @@ void FlowKillFlowRecyclerThread(void)
     while (tv != NULL) {
         if (strcasecmp(tv->name, "FlowRecyclerThread") == 0) {
             TmThreadsSetFlag(tv, THV_KILL);
-            TmThreadsSetFlag(tv, THV_DEINIT);
             cnt++;
+
+            /* value in seconds */
+#define THREAD_KILL_MAX_WAIT_TIME 60
+            /* value in microseconds */
+#define WAIT_TIME 100
+
+            double total_wait_time = 0;
+            while (!TmThreadsCheckFlag(tv, THV_RUNNING_DONE)) {
+                usleep(WAIT_TIME);
+                total_wait_time += WAIT_TIME / 1000000.0;
+                if (total_wait_time > THREAD_KILL_MAX_WAIT_TIME) {
+                    SCLogError(SC_ERR_FATAL, "Engine unable to "
+                            "disable detect thread - \"%s\".  "
+                            "Killing engine", tv->name);
+                    exit(EXIT_FAILURE);
+                }
+            }
         }
         tv = tv->next;
     }
@@ -957,24 +971,6 @@ void FlowKillFlowRecyclerThread(void)
     for (u = 0; u < flowrec_number; u++)
         SCCtrlCondSignal(&flow_recycler_ctrl_cond);
 
-    tv = tv_root[TVT_MGMT];
-    while (tv != NULL) {
-        if (strcasecmp(tv->name, "FlowRecyclerThread") == 0) {
-            /* be sure it has shut down */
-            while (!TmThreadsCheckFlag(tv, THV_CLOSED)) {
-                usleep(100);
-            }
-        }
-        tv = tv->next;
-    }
-
-
-    /* not possible, unless someone decides to rename FlowManagerThread */
-    if (cnt == 0) {
-        SCMutexUnlock(&tv_root_lock);
-        abort();
-    }
-
     SCMutexUnlock(&tv_root_lock);
 
     /* reset count, so we can kill and respawn (unix socket) */
diff --git a/src/flow-manager.h b/src/flow-manager.h
index a2e6f6dc06..32ae2b2641 100644
--- a/src/flow-manager.h
+++ b/src/flow-manager.h
@@ -30,7 +30,7 @@ SCCtrlMutex flow_manager_ctrl_mutex;
 #define FlowWakeupFlowManagerThread() SCCtrlCondSignal(&flow_manager_ctrl_cond)
 
 void FlowManagerThreadSpawn(void);
-void FlowKillFlowManagerThread(void);
+void FlowDisableFlowManagerThread(void);
 void FlowMgrRegisterTests (void);
 
 /** flow recycler scheduling condition */
@@ -40,7 +40,7 @@ SCCtrlMutex flow_recycler_ctrl_mutex;
     SCCtrlCondSignal(&flow_recycler_ctrl_cond)
 
 void FlowRecyclerThreadSpawn(void);
-void FlowKillFlowRecyclerThread(void);
+void FlowDisableFlowRecyclerThread(void);
 
 void TmModuleFlowManagerRegister (void);
 void TmModuleFlowRecyclerRegister (void);
diff --git a/src/flow-timeout.c b/src/flow-timeout.c
index afd1ef71cd..f2eb089928 100644
--- a/src/flow-timeout.c
+++ b/src/flow-timeout.c
@@ -553,11 +553,8 @@ static inline void FlowForceReassemblyForHash(void)
  */
 void FlowForceReassembly(void)
 {
-    /* called by 'main()' which has no packet pool */
-    PacketPoolInit();
     /* Carry out flow reassembly for unattended flows */
     FlowForceReassemblyForHash();
-    PacketPoolDestroy();
     return;
 }
 
diff --git a/src/runmode-unix-socket.c b/src/runmode-unix-socket.c
index 1d6b023fea..42f836cf22 100644
--- a/src/runmode-unix-socket.c
+++ b/src/runmode-unix-socket.c
@@ -283,13 +283,16 @@ TmEcode UnixSocketPcapFilesCheck(void *data)
         }
         this->currentfile = NULL;
 
+        /* needed by FlowForceReassembly */
+        PacketPoolInit();
+
         /* handle graceful shutdown of the flow engine, it's helper
          * threads and the packet threads */
-        FlowKillFlowManagerThread();
+        FlowDisableFlowManagerThread();
         TmThreadDisableReceiveThreads();
         FlowForceReassembly();
         TmThreadDisablePacketThreads();
-        FlowKillFlowRecyclerThread();
+        FlowDisableFlowRecyclerThread();
 
         /* kill the stats threads */
         TmThreadKillThreadsFamily(TVT_MGMT);
@@ -299,6 +302,8 @@ TmEcode UnixSocketPcapFilesCheck(void *data)
         TmThreadKillThreadsFamily(TVT_PPT);
         TmThreadClearThreadsFamily(TVT_PPT);
 
+        PacketPoolDestroy();
+
         /* mgt and ppt threads killed, we can run non thread-safe
          * shutdown functions */
         SCPerfReleaseResources();
diff --git a/src/suricata.c b/src/suricata.c
index 08f84cdc5e..60bf9ed025 100644
--- a/src/suricata.c
+++ b/src/suricata.c
@@ -2407,14 +2407,18 @@ int main(int argc, char **argv)
     UnixSocketKillSocketThread();
 
     if (suri.run_mode != RUNMODE_UNIX_SOCKET) {
-        /* First we need to kill the flow manager thread */
-        FlowKillFlowManagerThread();
+        /* First we need to disable the flow manager thread */
+        FlowDisableFlowManagerThread();
     }
 
+
     /* Disable packet acquisition first */
     TmThreadDisableReceiveThreads();
 
     if (suri.run_mode != RUNMODE_UNIX_SOCKET) {
+        /* we need a packet pool for FlowForceReassembly */
+        PacketPoolInit();
+
         FlowForceReassembly();
         /* kill receive threads when they have processed all
          * flow timeout packets */
@@ -2426,13 +2430,18 @@ int main(int argc, char **argv)
     /* before TmThreadKillThreads, as otherwise that kills it
      * but more slowly */
     if (suri.run_mode != RUNMODE_UNIX_SOCKET) {
-        FlowKillFlowRecyclerThread();
+        FlowDisableFlowRecyclerThread();
     }
 
     /* kill remaining threads */
     TmThreadKillThreads();
 
+
     if (suri.run_mode != RUNMODE_UNIX_SOCKET) {
+        /* destroy the packet pool for flow reassembly after all
+         * the other threads are gone. */
+        PacketPoolDestroy();
+
         SCPerfReleaseResources();
         IPPairShutdown();
         FlowShutdown();
diff --git a/src/tm-threads.c b/src/tm-threads.c
index 181d04a0b6..b7fb3a6957 100644
--- a/src/tm-threads.c
+++ b/src/tm-threads.c
@@ -352,11 +352,11 @@ void *TmThreadsSlotPktAcqLoop(void *td)
     /* process all pseudo packets the flow timeout may throw at us */
     TmThreadTimeoutLoop(tv, s);
 
-    PacketPoolDestroy();
-
     TmThreadsSetFlag(tv, THV_RUNNING_DONE);
     TmThreadWaitForFlag(tv, THV_DEINIT);
 
+    PacketPoolDestroy();
+
     for (slot = s; slot != NULL; slot = slot->slot_next) {
         if (slot->SlotThreadExitPrintStats != NULL) {
             slot->SlotThreadExitPrintStats(tv, SC_ATOMIC_GET(slot->slot_data));