diff --git a/core/src/net/sf/openrocket/rocketcomponent/FlightConfiguration.java b/core/src/net/sf/openrocket/rocketcomponent/FlightConfiguration.java
index 10c302735..78ce41f66 100644
--- a/core/src/net/sf/openrocket/rocketcomponent/FlightConfiguration.java
+++ b/core/src/net/sf/openrocket/rocketcomponent/FlightConfiguration.java
@@ -146,6 +146,34 @@ public class FlightConfiguration implements FlightConfigurableParameter<FlightCo
 		updateMotors();
 		updateActiveInstances();
 	}
+
+	/**
+	 * This method clears a stage and all stages below (higher stage number)
+	 *
+	 * @param stageNumber first stage number to turn off
+	 */
+	public void clearStagesBelow(int stageNumber) {
+		// I can't just use _setStageActive(stageNumber, false, true)
+		// because that won't clear side boosters' active flags (should it?)
+		for (int i = stageNumber; i < rocket.getStageCount(); i++) {
+			_setStageActive(i, false, false);
+		}
+		updateMotors();
+		updateActiveInstances();
+	}
+
+	/**
+	 * This method clears all stages above (but not including) a stage
+	 *
+	 * @param stageNumber first stage number to stay active
+	 */
+	public void clearStagesAbove(int stageNumber) {
+		for (int i = 0; i < stageNumber; i++) {
+			_setStageActive(i, false, false);
+		}
+		updateMotors();
+		updateActiveInstances();
+	}
 	
 	/**
 	 * Activates all stages as active starting from the specified component
@@ -187,7 +215,7 @@ public class FlightConfiguration implements FlightConfigurableParameter<FlightCo
 	}
 
 	/**
-	 * This method flags the specified stage as requested.  Other stages are unaffected.
+	 * This method flags the specified stage as requested.  Substages may be affected, depending on third parameter
 	 *
 	 * @param stageNumber   stage number to flag
 	 * @param _active       inactive (<code>false</code>) or active (<code>true</code>)
diff --git a/core/src/net/sf/openrocket/simulation/BasicEventSimulationEngine.java b/core/src/net/sf/openrocket/simulation/BasicEventSimulationEngine.java
index fd864e789..5212790b8 100644
--- a/core/src/net/sf/openrocket/simulation/BasicEventSimulationEngine.java
+++ b/core/src/net/sf/openrocket/simulation/BasicEventSimulationEngine.java
@@ -305,6 +305,9 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 			if (event.getSource() != null && event.getSource().getParent() != null &&
 					!currentStatus.getConfiguration().isComponentActive(event.getSource())) {
 				log.trace("Ignoring event from unattached component");
+				log.debug("    source " + event.getSource());
+				log.debug("    parent " + event.getSource().getParent());
+				log.debug("    active " + currentStatus.getConfiguration().isComponentActive(event.getSource()));
 				continue;
 			}
 			
@@ -381,7 +384,6 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 				}
 
 				// and queue up the burnout for this motor, as well. 
-//				double duration = motorState.getMotor().getBurnTimeEstimate();
 				double duration = motorState.getBurnTime();
 				double burnout = currentStatus.getSimulationTime() + duration;
 				addEvent(new FlightEvent(FlightEvent.Type.BURNOUT, burnout,
@@ -436,19 +438,24 @@ public class BasicEventSimulationEngine implements SimulationEngine {
 			case STAGE_SEPARATION: {
 				RocketComponent boosterStage = event.getSource();
 				final int stageNumber = boosterStage.getStageNumber();
+				log.debug("separating at stage " + stageNumber);
 
 				if (currentStatus.getConfiguration().isStageActive(stageNumber-1)) {
 					// Record the event.
 					currentStatus.getFlightData().addEvent(event);
 
-					// Mark the status as having dropped the booster
-					currentStatus.getConfiguration().clearStage( stageNumber);
-					
-					// Prepare the simulation branch
+					// Create a new simulation branch for the booster
 					SimulationStatus boosterStatus = new SimulationStatus(currentStatus);
+					
+					// Prepare the new simulation branch
 					boosterStatus.setFlightData(new FlightDataBranch(boosterStage.getName(), FlightDataType.TYPE_TIME));
-					// Mark the booster status as only having the booster.
-					boosterStatus.getConfiguration().setOnlyStage(stageNumber);
+
+					// Mark the current status as having dropped the current stage and all stages below it
+					currentStatus.getConfiguration().clearStagesBelow( stageNumber);
+					
+					// Mark the booster status as having no active stages above
+					boosterStatus.getConfiguration().clearStagesAbove(stageNumber);
+					
 					toSimulate.push(boosterStatus);
 					log.info(String.format("==>> @ %g; from Branch: %s ---- Branching: %s ---- \n",
 										   currentStatus.getSimulationTime(),