diff --git a/hyracks/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/impls/LSMHarness.java b/hyracks/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/impls/LSMHarness.java
index 1cc5143..06a3088 100644
--- a/hyracks/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/impls/LSMHarness.java
+++ b/hyracks/hyracks-storage-am-lsm-common/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/common/impls/LSMHarness.java
@@ -102,6 +102,8 @@
                 // Changing the flush status should *always* precede changing the mutable component.
                 lsmIndex.changeFlushStatusForCurrentMutableCompoent(false);
                 lsmIndex.changeMutableComponent();
+                // Notify all waiting threads whenever a flush has been scheduled since they will check 
+                // again if they can grab and enter the mutable component.
                 opTracker.notifyAll();
                 break;
             default:
@@ -130,6 +132,10 @@
                                 break;
                             case INACTIVE:
                                 ((AbstractMemoryLSMComponent) c).reset();
+                                // Notify all waiting threads whenever the mutable component's has change to inactive. This is important because
+                                // even though we switched the mutable components, it is possible that the component that we just switched
+                                // to is still busy flushing its data to disk. Thus, the notification that was issued upon scheduling the flush
+                                // is not enough. 
                                 opTracker.notifyAll();
                                 break;
                             default:
diff --git a/hyracks/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/LSMRTreeWithAntiMatterTuples.java b/hyracks/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/LSMRTreeWithAntiMatterTuples.java
index c095244..89d8516 100644
--- a/hyracks/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/LSMRTreeWithAntiMatterTuples.java
+++ b/hyracks/hyracks-storage-am-lsm-rtree/src/main/java/edu/uci/ics/hyracks/storage/am/lsm/rtree/impls/LSMRTreeWithAntiMatterTuples.java
@@ -249,8 +249,7 @@
         LSMRTreeOpContext rctx = createOpContext(NoOpOperationCallback.INSTANCE);
         rctx.setOperation(IndexOperation.MERGE);
         List<ILSMComponent> mergingComponents = ctx.getComponentHolder();
-        rctx.getComponentHolder().addAll(mergingComponents);
-        ITreeIndexCursor cursor = new LSMRTreeWithAntiMatterTuplesSearchCursor(ctx);
+        ITreeIndexCursor cursor = new LSMRTreeWithAntiMatterTuplesSearchCursor(rctx);
         LSMComponentFileReferences relMergeFileRefs = getMergeTargetFileName(mergingComponents);
         ILSMIndexAccessorInternal accessor = new LSMRTreeWithAntiMatterTuplesAccessor(lsmHarness, rctx);
         ioScheduler.scheduleOperation(new LSMRTreeMergeOperation(accessor, mergingComponents, cursor, relMergeFileRefs