diff --git a/core/org.eclipse.cdt.core.win32.x86/os/win32/x86/pty.dll b/core/org.eclipse.cdt.core.win32.x86/os/win32/x86/pty.dll
index d814057c3b4..60d5b377614 100644
Binary files a/core/org.eclipse.cdt.core.win32.x86/os/win32/x86/pty.dll and b/core/org.eclipse.cdt.core.win32.x86/os/win32/x86/pty.dll differ
diff --git a/core/org.eclipse.cdt.core.win32.x86/os/win32/x86/winpty-agent.exe b/core/org.eclipse.cdt.core.win32.x86/os/win32/x86/winpty-agent.exe
index a2b6289a116..2a0cfe5b3f7 100644
Binary files a/core/org.eclipse.cdt.core.win32.x86/os/win32/x86/winpty-agent.exe and b/core/org.eclipse.cdt.core.win32.x86/os/win32/x86/winpty-agent.exe differ
diff --git a/core/org.eclipse.cdt.core.win32.x86_64/os/win32/x86_64/pty.dll b/core/org.eclipse.cdt.core.win32.x86_64/os/win32/x86_64/pty.dll
index dc05c116cc1..221ac7deab5 100644
Binary files a/core/org.eclipse.cdt.core.win32.x86_64/os/win32/x86_64/pty.dll and b/core/org.eclipse.cdt.core.win32.x86_64/os/win32/x86_64/pty.dll differ
diff --git a/core/org.eclipse.cdt.core.win32.x86_64/os/win32/x86_64/winpty-agent.exe b/core/org.eclipse.cdt.core.win32.x86_64/os/win32/x86_64/winpty-agent.exe
index a2b6289a116..75b49a1a402 100644
Binary files a/core/org.eclipse.cdt.core.win32.x86_64/os/win32/x86_64/winpty-agent.exe and b/core/org.eclipse.cdt.core.win32.x86_64/os/win32/x86_64/winpty-agent.exe differ
diff --git a/core/org.eclipse.cdt.core.win32/META-INF/MANIFEST.MF b/core/org.eclipse.cdt.core.win32/META-INF/MANIFEST.MF
index 361c7939742..71a80c55985 100644
--- a/core/org.eclipse.cdt.core.win32/META-INF/MANIFEST.MF
+++ b/core/org.eclipse.cdt.core.win32/META-INF/MANIFEST.MF
@@ -2,7 +2,7 @@ Manifest-Version: 1.0
 Bundle-ManifestVersion: 2
 Bundle-Name: %fragmentName.win32
 Bundle-SymbolicName: org.eclipse.cdt.core.win32; singleton:=true
-Bundle-Version: 5.4.0.qualifier
+Bundle-Version: 5.4.1.qualifier
 Bundle-Vendor: %providerName
 Fragment-Host: org.eclipse.cdt.core.native;bundle-version="[5.7.0,6.0.0)"
 Bundle-Localization: plugin
diff --git a/core/org.eclipse.cdt.core.win32/library/pty/jni/src/pty.cpp b/core/org.eclipse.cdt.core.win32/library/pty/jni/src/pty.cpp
index d7d076ed2f3..a9865b0ad29 100644
--- a/core/org.eclipse.cdt.core.win32/library/pty/jni/src/pty.cpp
+++ b/core/org.eclipse.cdt.core.win32/library/pty/jni/src/pty.cpp
@@ -1,9 +1,9 @@
 /*******************************************************************************
- * Copyright (c) 2013, 2014 Wind River Systems, Inc. and others.
- * All rights reserved. This program and the accompanying materials
- * are made available under the terms of the Eclipse Public License v1.0
- * which accompanies this distribution, and is available at
- * http://www.eclipse.org/legal/epl-v10.html
+ * Copyright (c) 2013, 2016 Wind River Systems, Inc. and others.
+ * All rights reserved. This program and the accompanying materials
+ * are made available under the terms of the Eclipse Public License v1.0
+ * which accompanies this distribution, and is available at
+ * http://www.eclipse.org/legal/epl-v10.html
  *
  * Contributors:
  * Wind River Systems - initial API and implementation
@@ -145,7 +145,7 @@ JNIEXPORT jint JNICALL Java_org_eclipse_cdt_utils_pty_PTYInputStream_read0
             if (!ret || amount == 0)
                 amount = -1;
 
-            if (!ret) {
+            if (!ret && fd2pty.find(fd) != fd2pty.end()) {
                 int rc = winpty_get_exit_code(winpty);
                 fd2rc.insert(std::pair<int, int>(fd, rc));
             }
@@ -173,11 +173,11 @@ JNIEXPORT jint JNICALL Java_org_eclipse_cdt_utils_pty_PTYInputStream_close0(JNIE
     fd2pty_Iter = fd2pty.find(fd);
     if (fd2pty_Iter != fd2pty.end()) {
         winpty_t* winpty = fd2pty_Iter -> second;
+        fd2pty.erase(fd2pty_Iter);
 	    if (winpty != NULL) {
 		    winpty_close(winpty);
 		    winpty = NULL;
 	    }
-        fd2pty.erase(fd2pty_Iter);
     }
 
 	return 0;
@@ -241,11 +241,11 @@ JNIEXPORT jint JNICALL Java_org_eclipse_cdt_utils_pty_PTYOutputStream_close0(JNI
     fd2pty_Iter = fd2pty.find(fd);
     if (fd2pty_Iter != fd2pty.end()) {
         winpty_t* winpty = fd2pty_Iter -> second;
+        fd2pty.erase(fd2pty_Iter);
 	    if (winpty != NULL) {
 		    winpty_close(winpty);
     		winpty = NULL;
     	}
-        fd2pty.erase(fd2pty_Iter);
     }
 
 	return 0;
diff --git a/core/org.eclipse.cdt.core.win32/pom.xml b/core/org.eclipse.cdt.core.win32/pom.xml
index b2c6e51784f..69a6499f1f7 100644
--- a/core/org.eclipse.cdt.core.win32/pom.xml
+++ b/core/org.eclipse.cdt.core.win32/pom.xml
@@ -11,7 +11,7 @@
 		<relativePath>../../pom.xml</relativePath>
 	</parent>
 
-	<version>5.4.0-SNAPSHOT</version>
+	<version>5.4.1-SNAPSHOT</version>
 	<artifactId>org.eclipse.cdt.core.win32</artifactId>
 	<packaging>eclipse-plugin</packaging>