diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
index 0ef2f7acd..14fc4c754 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/ConstrainedMateFixingManager.java
@@ -7,10 +7,7 @@ import org.broadinstitute.sting.utils.GenomeLoc;
 import org.broadinstitute.sting.utils.GenomeLocParser;
 import org.broadinstitute.sting.utils.exceptions.UserException;
 
-import java.util.HashMap;
-import java.util.Map;
-import java.util.PriorityQueue;
-import java.util.Queue;
+import java.util.*;
 
 /*
  * Copyright (c) 2009 The Broad Institute
@@ -169,16 +166,17 @@ public class ConstrainedMateFixingManager {
         return pos + 2 * MAX_POS_MOVE_ALLOWED < addedRead.getAlignmentStart();
     }
 
-    private void writeRead(SAMRecord read) {
-        try {
-            writer.addAlignment(read);
-        } catch (IllegalArgumentException e) {
-            throw new UserException("If the maximum allowable reads in memory is too small, it may cause reads to be written out of order when trying to write the BAM; please see the --maxReadsInMemory argument for details.  " + e.getMessage(), e);
-        }
+    public void addRead(SAMRecord newRead, boolean readWasModified) {
+        addRead(newRead, readWasModified, true);
     }
 
-    public void addRead(SAMRecord newRead, boolean readWasModified) {
-        if ( DEBUG ) logger.info("New read pos " + newRead.getAlignmentStart() + " OP = " + newRead.getAttribute("OP"));
+    public void addReads(List<SAMRecord> newReads, Set<SAMRecord> modifiedReads) {
+        for ( SAMRecord newRead : newReads )
+            addRead(newRead, modifiedReads.contains(newRead), false);
+    }
+
+    private void addRead(SAMRecord newRead, boolean readWasModified, boolean canFlush) {
+        if ( DEBUG ) logger.info("New read pos " + newRead.getAlignmentStart() + " OP = " + newRead.getAttribute("OP") + " " + readWasModified);
 
         //final long curTime = timer.currentTime();
         //if ( curTime - lastProgressPrintTime > PROGRESS_PRINT_FREQUENCY ) {
@@ -188,7 +186,7 @@ public class ConstrainedMateFixingManager {
 
         // if the new read is on a different contig or we have too many reads, then we need to flush the queue and clear the map
         boolean tooManyReads = getNReadsInQueue() >= MAX_RECORDS_IN_MEMORY;
-        if ( tooManyReads || (getNReadsInQueue() > 0 && !waitingReads.peek().getReferenceIndex().equals(newRead.getReferenceIndex())) ) {
+        if ( canFlush && (tooManyReads || (getNReadsInQueue() > 0 && !waitingReads.peek().getReferenceIndex().equals(newRead.getReferenceIndex()))) ) {
             if ( DEBUG ) logger.warn("Flushing queue on " + (tooManyReads ? "too many reads" : ("move to new contig: " + newRead.getReferenceName() + " from " + waitingReads.peek().getReferenceName())) + " at " + newRead.getAlignmentStart());
 
             while ( getNReadsInQueue() > 1 ) {
@@ -279,6 +277,14 @@ public class ConstrainedMateFixingManager {
         }
     }
 
+    private void writeRead(SAMRecord read) {
+        try {
+            writer.addAlignment(read);
+        } catch (IllegalArgumentException e) {
+            throw new UserException("If the maximum allowable reads in memory is too small, it may cause reads to be written out of order when trying to write the BAM; please see the --maxReadsInMemory argument for details.  " + e.getMessage(), e);
+        }
+    }
+
     /**
      * @param read  the read
      * @return true if the read shouldn't be moved given the constraints of this SAMFileWriter
diff --git a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
index 425fd62ef..052e6363b 100755
--- a/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
+++ b/java/src/org/broadinstitute/sting/gatk/walkers/indels/IndelRealigner.java
@@ -416,8 +416,16 @@ public class IndelRealigner extends ReadWalker<Integer, Integer> {
         // pre-merge lists to sort them in preparation for constrained SAMFileWriter
         readsNotToClean.addAll(readsToClean.getReads());
         ReadUtils.coordinateSortReads(readsNotToClean);
-        for ( SAMRecord read : readsNotToClean )
-            emit(read);
+        if ( N_WAY_OUT == null ) {
+            manager.addReads(readsNotToClean, readsActuallyCleaned);
+        } else {
+            // in this case, it is possible to have the following scenario: the realigner gets permission to realign,
+            // the cache in the ConstrainedMateFixingManager gets filled up while emitting reads, and then the
+            // first-of-pair mates of realigned reads don't get fixed because they were flushed out of the queue too early.
+            // Since the N-way option is @hidden, I'm not interested in fixing this right now.
+            for ( SAMRecord read : readsNotToClean )
+                emit(read);
+        }
         readsToClean.clear();
         readsNotToClean.clear();
         readsActuallyCleaned.clear();