diff --git a/lib/Slic3r/GUI/3DScene.pm b/lib/Slic3r/GUI/3DScene.pm
index 8ecf10de7..b884a3548 100644
--- a/lib/Slic3r/GUI/3DScene.pm
+++ b/lib/Slic3r/GUI/3DScene.pm
@@ -319,6 +319,7 @@ sub _variable_layer_thickness_action {
     if ($self->{layer_height_edit_last_object_id} != -1) {
         # Mark the volume as modified, so Print will pick its layer height profile? Where to mark it?
         # Start a timer to refresh the print? schedule_background_process() ?
+        # The PrintObject::adjust_layer_height_profile() call adjusts the profile of its associated ModelObject, it does not modify the profile of the PrintObject itself.
         $self->{print}->get_object($self->{layer_height_edit_last_object_id})->adjust_layer_height_profile(
             $self->{layer_height_edit_last_z},
             $self->{layer_height_edit_strength},
diff --git a/lib/Slic3r/GUI/Plater.pm b/lib/Slic3r/GUI/Plater.pm
index f4dd41526..5a215edeb 100644
--- a/lib/Slic3r/GUI/Plater.pm
+++ b/lib/Slic3r/GUI/Plater.pm
@@ -116,8 +116,7 @@ sub new {
         });
         $self->{canvas3D}->set_on_model_update(sub {
             if ($Slic3r::GUI::Settings->{_}{background_processing}) {
-                $self->{apply_config_timer}->Stop if defined $self->{apply_config_timer};
-                $self->async_apply_config();
+                $self->schedule_background_process;
             } else {
                 # Hide the print info box, it is no more valid.
                 $self->{"print_info_box_show"}->(0);
diff --git a/slic3r.pl b/slic3r.pl
index 681b2fa6d..0cd814ce5 100755
--- a/slic3r.pl
+++ b/slic3r.pl
@@ -214,8 +214,11 @@ if (@ARGV) {  # slicing from command line
             output_file     => $opt{output},
         );
         
+        # This is delegated to C++ PrintObject::apply_config().
         $sprint->apply_config($config);
         $sprint->set_model($model);
+        # Do the apply_config once again to validate the layer height profiles at all the newly added PrintObjects.
+        $sprint->apply_config($config);
         
         if ($opt{export_svg}) {
             $sprint->export_svg;
diff --git a/xs/src/libslic3r/Print.cpp b/xs/src/libslic3r/Print.cpp
index 1fef7e731..e570abc4c 100644
--- a/xs/src/libslic3r/Print.cpp
+++ b/xs/src/libslic3r/Print.cpp
@@ -397,6 +397,16 @@ bool Print::apply_config(DynamicPrintConfig config)
         PrintObjectConfig new_config = this->default_object_config;
         // we override the new config with object-specific options
         normalize_and_apply_config(new_config, object->model_object()->config);
+        // Force a refresh of a variable layer height profile at the PrintObject if it is not valid.
+        if (! object->layer_height_profile_valid) {
+            // The layer_height_profile is not valid for some reason (updated by the user or invalidated due to some option change).
+            // Invalidate the slicing step, which in turn invalidates everything.
+            object->invalidate_step(posSlice);
+            // Following line sets the layer_height_profile_valid flag.
+            object->update_layer_height_profile();
+            // Trigger recalculation.
+            invalidated = true;
+        }
         // check whether the new config is different from the current one
         t_config_option_keys diff = object->config.diff(new_config);
         object->config.apply(new_config, diff, true);
@@ -475,22 +485,6 @@ exit_for_rearrange_regions:
             this->objects.back()->update_layer_height_profile();
         }
         invalidated = true;
-    } else {
-        // Check validity of the layer height profiles.
-        for (PrintObject *object : this->objects) {
-            if (! object->layer_height_profile_valid) {
-                // The layer_height_profile is not valid for some reason (updated by the user or invalidated due to some option change).
-                // Start slicing of this object from scratch.
-                object->invalidate_all_steps();
-                // Following line sets the layer_height_profile_valid flag.
-                object->update_layer_height_profile();
-                invalidated = true;
-            } else if (! step_done(posSlice)) {
-                // Update layer_height_profile from the main thread as it may pull the data from the associated ModelObject.
-                // Only update if the slicing was not finished yet.
-                object->update_layer_height_profile();
-            }
-        }
     }
     
     return invalidated;
@@ -585,11 +579,13 @@ std::string Print::validate() const
                 return "The Wipe Tower is only supported for multiple objects if they are printed with the same support_material_contact_distance";
             if (! equal_layering(slicing_params, slicing_params0))
                 return "The Wipe Tower is only supported for multiple objects if they are sliced equally.";
+            bool was_layer_height_profile_valid = object->layer_height_profile_valid;
             object->update_layer_height_profile();
+            object->layer_height_profile_valid = was_layer_height_profile_valid;
             for (size_t i = 1; i < object->layer_height_profile.size(); i += 2)
                 if (object->layer_height_profile[i-1] > slicing_params.object_print_z_min + EPSILON &&
                     std::abs(object->layer_height_profile[i] - object->config.layer_height) > EPSILON)
-                return "The Wipe Tower is currently only supported with constant Z layer spacing. Layer editing is not allowed.";
+                    return "The Wipe Tower is currently only supported with constant Z layer spacing. Layer editing is not allowed.";
         }
     }
     
diff --git a/xs/src/libslic3r/PrintObject.cpp b/xs/src/libslic3r/PrintObject.cpp
index 08a825421..ee7d9cb19 100644
--- a/xs/src/libslic3r/PrintObject.cpp
+++ b/xs/src/libslic3r/PrintObject.cpp
@@ -263,6 +263,7 @@ bool PrintObject::invalidate_step(PrintObjectStep step)
     } else if (step == posSlice) {
         invalidated |= this->invalidate_step(posPerimeters);
         invalidated |= this->invalidate_step(posSupportMaterial);
+        invalidated |= this->_print->invalidate_step(psWipeTower);
     } else if (step == posSupportMaterial) {
         invalidated |= this->_print->invalidate_step(psSkirt);
         invalidated |= this->_print->invalidate_step(psBrim);
@@ -1079,7 +1080,6 @@ void PrintObject::_slice()
     {
         this->clear_layers();
         // Object layers (pairs of bottom/top Z coordinate), without the raft.
-        this->update_layer_height_profile();
         std::vector<coordf_t> object_layers = generate_object_layers(slicing_params, this->layer_height_profile);
         // Reserve object layers for the raft. Last layer of the raft is the contact layer.
         int id = int(slicing_params.raft_layers());