Failures with windows security requirements and binaries installed

We are in the process of getting our application certified for Windows Server 2012 for Gold certification and running into the following 2 issues:
1. Failure for "Applications must comply with Windows security requirements".
Looks like the MPR tool is trying to scan some .log files and .xml files when the test is running and these are being used/locked by the application at that time. So these are listed under "Checks that didn't complete". attached is a screenshot
of this.
2. Failure for "Were any binaries installed for this Component"
This is the log message for "No binaries were detected as installed". Ours is a Java app and Java binaries are the only executables.
======================================================================
Log generated by Microsoft Platform Ready Test Tool - Version 4.1.0.0 | Signed: Tuesday, March 26, 2013
======================================================================
Test name: PPSS 3.23 Gold
Test date: 05/01/2013 13:11:54
Tested on: Virtual Machine on Microsoft Windows Server 2012 Hyper-V
Test for: Windows Server 2012
======================================================================
Test case/Verification: 11.1.1 - Check if application installed binaries
======================================================================
To pass this test, binaries must have been installed for this Component by a method tester identified in the ‘Setup Information’ screen.
To validate an actual test was conducted, a waiver must be filed.
The Windows Server Logo Program requires a complete but brief, technically detailed explanation of the application/solution, installation method, and hosted platform (ex: IIS, SharePoint, etc.).
Document any client components, besides Internet Explorer. ISV client components must also be tested with MPR Tool, on either Client or Server OS concurrently.
Waiver link may be found on MPR Tool or on Windows Server Logo Program website.
======================================================================
Result: No binaries were detected as installed.
05/01/2013 13:11:54 ::
======================================================================
05/01/2013 13:11:54 :: Note: The files below were excluded from this test
======================================================================
C:\Windows\Installer\cce9a8.msi
======================================================================
Test case/Verification: 11.1.1 - Check if application installed binaries
05/01/2013 13:11:54 End of Log.
======================================================================
QUESTIONS:
How can we resolve these issues?
Is passing these 2 failures mandatory in order to get certified?
Can we file a waiver for these?
Thanks,
Neeha.

Update: We were not giving the right installation directory and corrected that.
After changing the installation directory, we end up with these 2 failures:
Log message for Binaries installed is below. As mentioned in the message above, ours is a Java application that does not have any binaries installed.
Can we submit a waiver for this?
=====================================================================
Log generated by Microsoft Platform Ready Test Tool - Version 4.1.0.0 | Signed: Tuesday, March 26, 2013
======================================================================
Test name: PPSS 3.23 Gold Certification
Test date: 05/06/2013 12:56:03
Tested on: Virtual Machine on Microsoft Windows Server 2012 Hyper-V
Test for: Windows Server 2012
======================================================================
Test case/Verification: 11.1.1 - Check if application installed binaries
======================================================================
To pass this test, binaries must have been installed for this Component by a method tester identified in the ‘Setup Information’ screen.
To validate an actual test was conducted, a waiver must be filed.
The Windows Server Logo Program requires a complete but brief, technically detailed explanation of the application/solution, installation method, and hosted platform (ex: IIS, SharePoint, etc.).
Document any client components, besides Internet Explorer. ISV client components must also be tested with MPR Tool, on either Client or Server OS concurrently.
Waiver link may be found on MPR Tool or on Windows Server Logo Program website.
======================================================================
Result: No binaries were detected as installed.
05/06/2013 12:56:03 ::
======================================================================
05/06/2013 12:56:03 :: Note: The files below were excluded from this test
======================================================================
C:\Windows\Installer\1ab2aa62.msi
======================================================================
Test case/Verification: 11.1.1 - Check if application installed binaries
05/06/2013 12:56:03 End of Log.
======================================================================
Log message for executables installed is below. Is a waiver needed for this? The highlighted part of the log message talks about not needing a waiver for the optional test. Is it talking about 3rd party binaries alone?
======================================================================
Log generated by Microsoft Platform Ready Test Tool - Version 4.1.0.0 | Signed: Tuesday, March 26, 2013
======================================================================
Test name: PPSS 3.23 Gold Certification
Test date: 05/06/2013 12:56:00
Tested on: Virtual Machine on Microsoft Windows Server 2012 Hyper-V
Test for: Windows Server 2012
======================================================================
Test case/Verification: TC2.3 - All binaries and installers must be Authenticode signed
======================================================================
Authenticode sign all setup files and binaries installed by the application.
Binaries not built by product group or company can be considered 3rd party.
3rd party binaries without valid signatures will fail this test case. No waiver is required for this optional test case.
======================================================================
05/06/2013 12:56:00 :: Binary list
No binary found for verification.
05/06/2013 12:56:00 ::
List of installers that failed signature verification:
C:\ppss_323_installer\install_PPSS_3_23_0\setup.exe
======================================================================
Note: The files below were excluded from this test
======================================================================
C:\Windows\Installer\1ab2aa62.msi
======================================================================
No executable files were detected as installed during test.
Microsoft Platform Ready Test Tool requires that your application physically installs executable files on this Computer.
======================================================================
Test case/Verification: TC2.3 - All binaries and installers must be Authenticode signed
05/06/2013 12:56:03 End of Log.
======================================================================
Any help of guidance in addressing these 2 issues will be great.
Thanks,
Neeha.

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