diff -r 8a9abb71988c core.startup/src/org/netbeans/core/startup/layers/BinaryFS.java
--- a/core.startup/src/org/netbeans/core/startup/layers/BinaryFS.java	Thu Jun 21 13:46:12 2012 +0200
+++ b/core.startup/src/org/netbeans/core/startup/layers/BinaryFS.java	Thu Jun 21 13:57:34 2012 +0200
@@ -87,6 +87,7 @@
 import org.openide.util.Lookup;
 import org.openide.util.NbBundle;
 import org.openide.util.SharedClassObject;
+import org.openide.util.Utilities;
 import org.openide.util.actions.SystemAction;
 import org.openide.util.io.NbObjectInputStream;
 
@@ -265,10 +266,10 @@
     }
     private static String toAbsoluteURL(String relURL) {
         if (relURL.startsWith("home@")) {
-            return "jar:file:" + System.getProperty("netbeans.home") + relURL.substring(5);
+            return toJarURI(System.getProperty("netbeans.home")) + relURL.substring(5);
         }
         if (relURL.startsWith("user@")) {
-            return "jar:file:" + System.getProperty("netbeans.user") + relURL.substring(5);
+            return toJarURI(System.getProperty("netbeans.user")) + relURL.substring(5);
         }
         if (relURL.startsWith("abs@")) {
             return "jar:file:" + relURL.substring(4);
@@ -278,7 +279,33 @@
             return relURL;
         }
         int cluster = Integer.parseInt(relURL.substring(0, indx));
-        return "jar:file:" + RelPaths.cluster(cluster) + relURL.substring(indx + 1);
+        return toJarURI(RelPaths.cluster(cluster)) + relURL.substring(indx + 1);
+    }
+
+    private static String toJarURI(String path) {
+        class DirFile extends File {
+            public DirFile(String pathname) {
+                super(pathname);
+            }
+
+            @Override
+            public boolean isDirectory() {
+                return true;
+            }
+
+            @Override
+            public boolean isFile() {
+                return false;
+            }
+
+            @Override
+            public File getAbsoluteFile() {
+                return this;
+            }
+        }
+        String ret = "jar:" + Utilities.toURI(new DirFile(path)).toString(); // NOI18N
+        assert !ret.contains("//") : ret;
+        return ret;
     }
     
     @Override
diff -r 8a9abb71988c core.startup/src/org/netbeans/core/startup/preferences/RelPaths.java
--- a/core.startup/src/org/netbeans/core/startup/preferences/RelPaths.java	Thu Jun 21 13:46:12 2012 +0200
+++ b/core.startup/src/org/netbeans/core/startup/preferences/RelPaths.java	Thu Jun 21 13:57:34 2012 +0200
@@ -72,21 +72,17 @@
             return null;
         }
         String[] ret = {null, null};
-        if (testWritePath(path, System.getProperty("netbeans.user"), "user", ret)) {
-            return ret;
-        }
+        testWritePath(path, System.getProperty("netbeans.user"), "user", ret); // NOI18N
         int cnt = 0;
         for (String p : dirs()) {
-            if (testWritePath(path, p, "" + cnt, ret)) {
-                return ret;
-            }
+            testWritePath(path, p, "" + cnt, ret);
             cnt++;
         }
-        if (testWritePath(path, System.getProperty("netbeans.home"), "home", ret)) {
-            return ret;
+        testWritePath(path, System.getProperty("netbeans.home"), "home", ret); // NOI18N
+        if (ret[1] == null) {
+            ret[0] = "abs"; // NOI18N
+            ret[1] = path;
         }
-        ret[0] = "abs";
-        ret[1] = path;
         return ret;
     }
     
@@ -144,8 +140,17 @@
             return false;
         }
         if (path.startsWith(prefix)) {
-            ret[0] = codeName;
-            ret[1] = path.substring(prefix.length());
+            String relPath = path.substring(prefix.length());
+            while (relPath.startsWith("/")) {
+                relPath = relPath.substring(1);
+            }
+            if (
+                ret[1] == null || 
+                ret[1].length() > relPath.length()
+            ) {
+                ret[0] = codeName;
+                ret[1] = relPath;
+            }
             return true;
         }
         return false;
@@ -154,7 +159,7 @@
     private static synchronized String[] dirs() {
         if (dirs == null) {
             List<String> tmp = new ArrayList<String>();
-            String nbdirs = System.getProperty("netbeans.dirs");
+            String nbdirs = System.getProperty("netbeans.dirs"); // NOI18N
             if (nbdirs != null) {
                 StringTokenizer tok = new StringTokenizer(nbdirs, File.pathSeparator);
                 while (tok.hasMoreTokens()) {
@@ -165,4 +170,8 @@
         }
         return dirs;
     }
+    
+    static synchronized void assignDirs(String... arr) {
+        dirs = arr;
+    }
 }
diff -r 8a9abb71988c core.startup/test/unit/src/org/netbeans/core/startup/preferences/RelPathsTest.java
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/core.startup/test/unit/src/org/netbeans/core/startup/preferences/RelPathsTest.java	Thu Jun 21 13:57:34 2012 +0200
@@ -0,0 +1,58 @@
+/*
+ * DO NOT ALTER OR REMOVE COPYRIGHT NOTICES OR THIS HEADER.
+ *
+ * Copyright 2012 Oracle and/or its affiliates. All rights reserved.
+ *
+ * Oracle and Java are registered trademarks of Oracle and/or its affiliates.
+ * Other names may be trademarks of their respective owners.
+ *
+ * The contents of this file are subject to the terms of either the GNU
+ * General Public License Version 2 only ("GPL") or the Common
+ * Development and Distribution License("CDDL") (collectively, the
+ * "License"). You may not use this file except in compliance with the
+ * License. You can obtain a copy of the License at
+ * http://www.netbeans.org/cddl-gplv2.html
+ * or nbbuild/licenses/CDDL-GPL-2-CP. See the License for the
+ * specific language governing permissions and limitations under the
+ * License.  When distributing the software, include this License Header
+ * Notice in each file and include the License file at
+ * nbbuild/licenses/CDDL-GPL-2-CP.  Oracle designates this
+ * particular file as subject to the "Classpath" exception as provided
+ * by Oracle in the GPL Version 2 section of the License file that
+ * accompanied this code. If applicable, add the following below the
+ * License Header, with the fields enclosed by brackets [] replaced by
+ * your own identifying information:
+ * "Portions Copyrighted [year] [name of copyright owner]"
+ *
+ * If you wish your version of this file to be governed by only the CDDL
+ * or only the GPL Version 2, indicate your decision by adding
+ * "[Contributor] elects to include this software in this distribution
+ * under the [CDDL or GPL Version 2] license." If you do not indicate a
+ * single choice of license, a recipient has the option to distribute
+ * your version of this file under either the CDDL, the GPL Version 2 or
+ * to extend the choice of license to its licensees as provided above.
+ * However, if you add GPL Version 2 code and therefore, elected the GPL
+ * Version 2 license, then the option applies only if the new code is
+ * made subject to such option by the copyright holder.
+ *
+ * Contributor(s):
+ *
+ * Portions Copyrighted 2012 Sun Microsystems, Inc.
+ */
+package org.netbeans.core.startup.preferences;
+
+import org.netbeans.junit.NbTestCase;
+
+public class RelPathsTest extends NbTestCase {
+    
+    public RelPathsTest(String s) {
+        super(s);
+    }
+    
+    public void testFindRelativePath() {
+        RelPaths.assignDirs("/root/java", "/root/javacard");
+        String[] arr = RelPaths.findRelativePath("/root/javacard/isMyFriend");
+        assertEquals("1", arr[0]);
+        assertEquals("isMyFriend", arr[1]);
+    }
+}