diff --git a/klippy/extras/input_shaper.py b/klippy/extras/input_shaper.py
index cb9027d98..c79cdcf2c 100644
--- a/klippy/extras/input_shaper.py
+++ b/klippy/extras/input_shaper.py
@@ -138,6 +138,7 @@ class InputShaper:
         if self.toolhead is None:
             # Klipper initialization is not yet completed
             return
+        self.toolhead.flush_step_generation()
         ffi_main, ffi_lib = chelper.get_ffi()
         kin = self.toolhead.get_kinematics()
         for s in kin.get_steppers():
@@ -146,8 +147,9 @@ class InputShaper:
             is_sk = self._get_input_shaper_stepper_kinematics(s)
             if is_sk is None:
                 continue
-            self.toolhead.flush_step_generation()
             ffi_lib.input_shaper_update_sk(is_sk)
+        motion_queuing = self.printer.lookup_object("motion_queuing")
+        motion_queuing.check_step_generation_scan_windows()
     def _update_input_shaping(self, error=None):
         self.toolhead.flush_step_generation()
         ffi_main, ffi_lib = chelper.get_ffi()
@@ -164,6 +166,8 @@ class InputShaper:
                     continue
                 if not shaper.set_shaper_kinematics(is_sk):
                     failed_shapers.append(shaper)
+        motion_queuing = self.printer.lookup_object("motion_queuing")
+        motion_queuing.check_step_generation_scan_windows()
         if failed_shapers:
             error = error or self.printer.command_error
             raise error("Failed to configure shaper(s) %s with given parameters"
diff --git a/klippy/extras/motion_queuing.py b/klippy/extras/motion_queuing.py
index a61ba5cc0..99035f06f 100644
--- a/klippy/extras/motion_queuing.py
+++ b/klippy/extras/motion_queuing.py
@@ -50,7 +50,6 @@ class PrinterMotionQueuing:
         if self.mcu.is_fileoutput():
             self.can_pause = False
         # Kinematic step generation scan window time tracking
-        self.need_calc_kin_flush_delay = True
         self.kin_flush_delay = SDS_CHECK_TIME
         # Register handlers
         printer.register_event_handler("klippy:shutdown", self._handle_shutdown)
@@ -129,8 +128,7 @@ class PrinterMotionQueuing:
     # Kinematic step generation scan window time tracking
     def get_kin_flush_delay(self):
         return self.kin_flush_delay
-    def _calc_kin_flush_delay(self):
-        self.need_calc_kin_flush_delay = False
+    def check_step_generation_scan_windows(self):
         ffi_main, ffi_lib = chelper.get_ffi()
         kin_flush_delay = SDS_CHECK_TIME
         for mcu, sc in self.stepcompress:
@@ -175,11 +173,8 @@ class PrinterMotionQueuing:
             if flush_time >= want_flush_time:
                 break
     def flush_all_steps(self):
-        self.need_calc_kin_flush_delay = True
         self.advance_flush_time(self.need_step_gen_time)
     def calc_step_gen_restart(self, est_print_time):
-        if self.need_calc_kin_flush_delay:
-            self._calc_kin_flush_delay()
         kin_time = max(est_print_time + MIN_KIN_TIME, self.last_step_gen_time)
         return kin_time + self.kin_flush_delay
     def _flush_handler(self, eventtime):
diff --git a/klippy/kinematics/extruder.py b/klippy/kinematics/extruder.py
index 4e6f14e41..9b1ec2d20 100644
--- a/klippy/kinematics/extruder.py
+++ b/klippy/kinematics/extruder.py
@@ -75,6 +75,8 @@ class ExtruderStepper:
             # Need full kinematic flush to change the smooth time
             toolhead.flush_step_generation()
             espa(self.sk_extruder, 0., pressure_advance, new_smooth_time)
+            motion_queuing = self.printer.lookup_object('motion_queuing')
+            motion_queuing.check_step_generation_scan_windows()
         else:
             toolhead.register_lookahead_callback(
                 lambda print_time: espa(self.sk_extruder, print_time,