diff --git a/src/harness/harness.ts b/src/harness/harness.ts
index 78546f81c73..10a87108d43 100644
--- a/src/harness/harness.ts
+++ b/src/harness/harness.ts
@@ -1340,8 +1340,8 @@ module Harness {
         export function getErrorBaseline(inputFiles: { unitName: string; content: string }[], diagnostics: ts.Diagnostic[]) {
             diagnostics.sort(ts.compareDiagnostics);
             let outputLines: string[] = [];
-            // Count up all the errors we find so we don't miss any
-            let totalErrorsReported = 0;
+            // Count up all errors that were found in files other than lib.d.ts so we don't miss any
+            let totalErrorsReportedInNonLibraryFiles = 0;
 
             function outputErrorText(error: ts.Diagnostic) {
                 let message = ts.flattenDiagnosticMessageText(error.messageText, Harness.IO.newLine());
@@ -1352,8 +1352,15 @@ module Harness {
                     .filter(s => s.length > 0)
                     .map(s => "!!! " + ts.DiagnosticCategory[error.category].toLowerCase() + " TS" + error.code + ": " + s);
                 errLines.forEach(e => outputLines.push(e));
-
-                totalErrorsReported++;
+                
+                // do not count errors from lib.d.ts here, they are computed separately as numLibraryDiagnostics
+                // if lib.d.ts is explicitly included in input files and there are some errors in it (i.e. because of duplicate identifiers) 
+                // then they will be added twice thus triggering 'total errors' assertion with condition
+                // 'totalErrorsReportedInNonLibraryFiles + numLibraryDiagnostics + numTest262HarnessDiagnostics, diagnostics.length
+                 
+                if (!error.file || !isLibraryFile(error.file.fileName)) {
+                    totalErrorsReportedInNonLibraryFiles++;
+                }
             }
 
             // Report global errors
@@ -1438,7 +1445,7 @@ module Harness {
             });
 
             // Verify we didn't miss any errors in total
-            assert.equal(totalErrorsReported + numLibraryDiagnostics + numTest262HarnessDiagnostics, diagnostics.length, "total number of errors");
+            assert.equal(totalErrorsReportedInNonLibraryFiles + numLibraryDiagnostics + numTest262HarnessDiagnostics, diagnostics.length, "total number of errors");
 
             return minimalDiagnosticsToString(diagnostics) +
                 Harness.IO.newLine() + Harness.IO.newLine() + outputLines.join("\r\n");
@@ -1816,11 +1823,11 @@ module Harness {
         return filePath.indexOf(Harness.libFolder) === 0;
     }
 
-    export function getDefaultLibraryFile(): { unitName: string, content: string } {
+    export function getDefaultLibraryFile(io: Harness.IO): { unitName: string, content: string } {
         let libFile = Harness.userSpecifiedRoot + Harness.libFolder + "lib.d.ts";
         return {
             unitName: libFile,
-            content: IO.readFile(libFile)
+            content: io.readFile(libFile)
         };
     }
 
diff --git a/src/harness/rwcRunner.ts b/src/harness/rwcRunner.ts
index c89a8b1d910..a1aaeed3d55 100644
--- a/src/harness/rwcRunner.ts
+++ b/src/harness/rwcRunner.ts
@@ -4,7 +4,7 @@
 /// <reference path="..\compiler\commandLineParser.ts"/>
 
 module RWC {
-    function runWithIOLog(ioLog: IOLog, fn: () => void) {
+    function runWithIOLog(ioLog: IOLog, fn: (oldIO: Harness.IO) => void) {
         let oldIO = Harness.IO;
 
         let wrappedIO = Playback.wrapIO(oldIO);
@@ -12,7 +12,7 @@ module RWC {
         Harness.IO = wrappedIO;
 
         try {
-            fn();
+            fn(oldIO);
         } finally {
             wrappedIO.endReplay();
             Harness.IO = oldIO;
@@ -32,9 +32,6 @@ module RWC {
             let baseName = /(.*)\/(.*).json/.exec(ts.normalizeSlashes(jsonPath))[2];
             let currentDirectory: string;
             let useCustomLibraryFile: boolean;
-            
-            const defaultLibraryFile = Harness.getDefaultLibraryFile();
-            
             after(() => {
                 // Mocha holds onto the closure environment of the describe callback even after the test is done.
                 // Therefore we have to clean out large objects after the test is done.
@@ -67,7 +64,7 @@ module RWC {
                     opts.options.noEmitOnError = false;
                 });
 
-                runWithIOLog(ioLog, () => {
+                runWithIOLog(ioLog, oldIO => {
                     harnessCompiler.reset();
 
                     // Load the files
@@ -77,7 +74,6 @@ module RWC {
 
                     // Add files to compilation
                     let isInInputList = (resolvedPath: string) => (inputFile: { unitName: string; content: string; }) => inputFile.unitName === resolvedPath;
-                    let prependDefaultLib = false;
                     for (let fileRead of ioLog.filesRead) {
                         // Check if the file is already added into the set of input files.
                         const resolvedPath = ts.normalizeSlashes(Harness.IO.resolvePath(fileRead.path));
@@ -101,15 +97,11 @@ module RWC {
                                 }
                                 else {
                                     // set the flag to put default library to the beginning of the list
-                                    prependDefaultLib = true;
+                                    inputFiles.unshift(Harness.getDefaultLibraryFile(oldIO));
                                 }
                             }
                         }
                     }
-                    
-                    if (prependDefaultLib) {
-                        inputFiles.unshift(defaultLibraryFile);
-                    }
 
                     // do not use lib since we already read it in above
                     opts.options.noLib = true;