diff --git a/platform/cooja/Makefile.cooja b/platform/cooja/Makefile.cooja
index 22cdd5260..1edba7d17 100644
--- a/platform/cooja/Makefile.cooja
+++ b/platform/cooja/Makefile.cooja
@@ -1,4 +1,4 @@
-# $Id: Makefile.cooja,v 1.26 2009/03/11 08:40:37 fros4943 Exp $
+# $Id: Makefile.cooja,v 1.27 2009/03/12 13:04:11 fros4943 Exp $
 
 ## The COOJA Simulator Contiki platform Makefile
 ##
@@ -34,7 +34,8 @@ $(CONTIKI)/tools/cooja/dist/cooja.jar:
 
 # Quickstart rule
 $(MAKECMDGOALS): $(CONTIKI)/tools/cooja/dist/cooja.jar
-	java -jar $(CONTIKI)/tools/cooja/dist/cooja.jar -quickstart=$(MAKECMDGOALS) -contiki=$(CONTIKI)
+	(cd $(CONTIKI)/tools/cooja/build && \
+	 java -jar ../dist/cooja.jar -quickstart='$(abspath $(firstword $(MAKECMDGOALS)))')
 
 endif ## QUICKSTART
 
@@ -96,6 +97,7 @@ ifdef REDEF_PRINTF
 endif ## REDEF_PRINTF
 	$(LINK_COMMAND_1) $^ $(LINK_COMMAND_2)
 
+.PHONY: $(CONTIKI_APP).cooja
 $(CONTIKI_APP).cooja: $(JNILIB)
 	cp $(JNILIB) $@
 	rm $(CONTIKI_APP_OBJ)
diff --git a/tools/cooja/java/se/sics/cooja/GUI.java b/tools/cooja/java/se/sics/cooja/GUI.java
index 2456a0fc2..4390cdc8b 100644
--- a/tools/cooja/java/se/sics/cooja/GUI.java
+++ b/tools/cooja/java/se/sics/cooja/GUI.java
@@ -24,7 +24,7 @@
  * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS
  * SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
  *
- * $Id: GUI.java,v 1.114 2009/03/11 20:14:52 fros4943 Exp $
+ * $Id: GUI.java,v 1.115 2009/03/12 13:04:10 fros4943 Exp $
  */
 
 package se.sics.cooja;
@@ -2878,12 +2878,18 @@ public class GUI extends Observable {
       String contikiApp = args[0].substring("-quickstart=".length());
 
       if (contikiApp.endsWith(".cooja")) {
-        contikiApp = contikiApp.substring(0, contikiApp.length() - 6);
+        contikiApp = contikiApp.substring(0, contikiApp.length() - ".cooja".length());
       }
       if (!contikiApp.endsWith(".c")) {
         contikiApp += ".c";
       }
 
+      /* Cygwin fix */
+      if (contikiApp.startsWith("/cygdrive/")) {
+        char driveCharacter = contikiApp.charAt("/cygdrive/".length());
+        contikiApp = contikiApp.replace("/cygdrive/" + driveCharacter + "/", driveCharacter + ":/");
+      }
+
       boolean ok = quickStartSimulation(contikiApp);
       if (!ok) {
         System.exit(1);