Index: modeshape-jcr/src/main/java/org/modeshape/jcr/JcrRepositoryFactory.java
===================================================================
--- modeshape-jcr/src/main/java/org/modeshape/jcr/JcrRepositoryFactory.java	(revision 2051)
+++ modeshape-jcr/src/main/java/org/modeshape/jcr/JcrRepositoryFactory.java	(working copy)
@@ -171,6 +171,19 @@ public class JcrRepositoryFactory implements RepositoryFactory {
         assert configUrl != null;
 
         synchronized (ENGINES) {
+            /*
+             * Strip any query parameters from the incoming file URLs by creating a new URL with the same protocol, host, and port,
+             * but using the URL path as returned by URL#getPath() instead of the URL path and query parameters as returned by URL#getFile().
+             */
+            if ("file".equals(configUrl.getProtocol())) {
+                try {
+                    configUrl = new URL(configUrl.getProtocol(), configUrl.getHost(), configUrl.getPort(), configUrl.getPath());
+                } catch (MalformedURLException mfe) {
+                    // This shouldn't be possible, since we're creating a new URL from an existing, valid URL
+                    throw new IllegalStateException(mfe);
+                }
+            }
+
             String configKey = configUrl.toString();
 
             JcrEngine engine = ENGINES.get(configKey);