Steps to reproduce the problem:
1. Add below testcase to chromium/src/android_webview/javatests/src/org/chromium/android_webview/test/WebViewModalDialogOverrideTest.java

2. Run the testcase with out/Release/bin/run_android_webview_test_apk -f WebViewModalDialogOverrideTest\#testAwContentsOnPauseDoesNotResumeJsTimers

-- <Java> ------------------------------------
    @SmallTest
    @Feature({"AndroidWebView"})
    public void testAwContentsOnPauseDoesNotResumeJsTimers() throws Throwable {
        final String alertText = "Hello World!";

        final AtomicBoolean callbackCalled = new AtomicBoolean(false);
        // Returning true from the callback should not show a dialog.
        TestAwContentsClient client = new TestAwContentsClient() {
            @Override
            public void handleJsAlert(String url, String message, JsResultReceiver res) {
                callbackCalled.set(true);
                res.confirm();
                assertEquals(alertText, message);
            }
        };
        AwTestContainerView view = createAwTestContainerViewOnMainSync(client);
        final AwContents awContents = view.getAwContents();

        enableJavaScriptOnUiThread(awContents);
        loadDataSync(awContents, client.getOnPageFinishedHelper(),
                EMPTY_PAGE, "text/html", false);
        JSUtils.executeJavaScriptAndWaitForResult(this, awContents,
                client.getOnEvaluateJavaScriptResultHelper(),
                "setTimeout(function(){alert('" + alertText + "');},1000)");

        // added pause timers
        getInstrumentation().runOnMainSync(new Runnable() {
            @Override
            public void run() {
                awContents.pauseTimers();
                awContents.onPause();
            }
        });

        SystemClock.sleep(2000);
        assertFalse(callbackCalled.get());
    }
-- </Java> ------------------------------------

2. testcase fails

What is the expected behavior?
Testcase should not fail.

What went wrong?
The awContents.onPause() call is causing 
the mContentViewCore.onHide() call, which un-pauses the JS timers.

Which is bad. I think.

Did this work before? N/A 

Chrome version: 49.0.2623.110  Channel: n/a
OS Version: 
Flash Version: not important

Test is low-quality, since it contains SystemClock.sleep 'n stuff, but it shows the problem.