Some Java applets do not work after silent installation, solved by toggling "Enable Java content in the browser" - Why?

Question

We have about 1,800 workstations running Windows 7 (both 32-bit and 64-bit) running various versions of the Java JRE from 6 update 32 through 7 update 51.  Most are on 6 update 45.  We would like to standardize on Java 7 update 51 (32-bit) and get everyone updated to that version for security reasons.
For the past two weeks, we have been having trouble with our installation pre-pilot.  What we are seeing is that our procedure successfully closes any open Internet Explorer windows and Java-related processes, uninstalls all old versions of the Java JRE, and then claims to have successfully installed Java 7 update 51.  The Java Control panel works.  We can even take Internet Explorer to Verify Java Version or Java Tester - What Version of Java Are You Running? and confirm that the Java applets on those sites are loading (though the latter only works after adding the site to the exceptions site list); however, when testers try to access our Kronos Workforce Central 6.3.10 system, the Java applets used by that system do not load.
We have tried the following things, none of which worked:
Clear Internet Explorer browser cache and cookies.
Clear the local Java cache.
Reboot the computer.
Reset Internet Explorer settings, including personal settings.
The one thing which does work is going into the Java Control Panel, going to the Security tab, unchecking "Enable Java content in the browser", pressing Apply, pressing OK on the pop-up window, checking the "Enable Java content in the browser" box again, pressing OK, pressing OK on the pop-up window, and then restarting Internet Explorer.  It is only after this point that all Java applets, including the ones used by Kronos Workforce Central 6.3.10, work.
What I need to know is how I can automate the procedure of reinitializing the "Enable Java content in the browser" checkbox after installation or am I doing something wrong or missing a step in the automated installation that is causing this to happen?
We are using Microsoft SCCM 2007 R3 to accomplish this upgrade, and everything is being run on the client machine using the SYSTEM account.  First, the PowerShell script "javaclean.ps1" is run, with part of the command-line process changing the PowerShell script execution policy to Bypass.  This script handles the closing of Java-dependent applications and Java processes and uninstalls old Java versions.
javaclean.ps1:
#Find all Java products excluding the auto updater which actually gets uninstalled when the main install is removed.
write-host "Searching for all installed Java versions" -ForegroundColor Yellow
[array]$javas=Get-WmiObject -query "select * from win32_Product where (Name like 'Java %' or Name like 'Java(TM)%' or Name like 'J2SE%') and Name <> 'Java Auto Updater'"
if ($javas.count -gt 0)
    write-host "Java is already Installed" -ForegroundColor Yellow
    #Get all the Java processes and kill them. If java is running and the processes aren't killed then this script will invoke a sudden reboot.
    [array]$processes=Get-Process -Name "Java*" #-erroraction silentlycontinue
    $processes += Get-Process -Name "iexplore" #-erroraction silentlycontinue
    $processes += Get-Process -Name "firefox" #-erroraction silentlycontinue
    $processes += Get-Process -Name "chrome" #-erroraction silentlycontinue
    $processes += Get-Process -Name "jqs" #-erroraction silentlycontinue
    $processes += Get-Process -Name "jusched" #-erroraction silentlycontinue
    $processes += Get-Process -Name "jp2launcher" #-erroraction silentlycontinue
    if ($processes.Count -gt 0)
        foreach ($myprocess in $processes)
            $myprocess.kill()
    #Loop through the installed Java products.
    foreach($java in $javas){
        write-host "Uninstalling "$java.name -ForegroundColor Yellow
        $java.Uninstall()
After this script is complete, SCCM calls a the VBS script "install.vbs" to perform the actual installation of Java JRE 7 update 51.
install.vbs
'* Script: Install JRE 7 routine
'* Date:   3/14/14
'* Author: [REDACTED]
'* Rev:    1.0
'* Notes: 
'/// Common
Set objFSO = CreateObject("Scripting.FileSystemObject")
Set objWshShell = CreateObject("WScript.Shell")
' Get system architecture
Dim colSys : Set colSys = GetObject("WinMGMTS://").ExecQuery("SELECT AddressWidth FROM Win32_Processor",, 48)
Dim objSys
For Each objSys In colSys
    If objSys.AddressWidth = 64 Then bolIs64Bit = True
Next
' Get operating system
Dim colOS : Set colOS = GetObject("WinMGMTS://").ExecQuery ("Select * from Win32_OperatingSystem",,48)
Dim objOS
For Each objOS In colOS
    If Left(objOS.caption, 20) = "Microsoft Windows 8 " Then
        bolIsWin8 = True
        WScript.Echo "win8"
    End If
    If Left(objOS.caption, 22) = "Microsoft Windows 8.1 " Then
        bolIsWin81 = True
        WScript.Echo "win81"
    End    If
Next
' Set 32 bit program files directory
If bolIs64Bit = True Then
    strPFILES = "Program Files (x86)"
    strSYSDIR = "SysWOW64"
    Else strPFILES = "Program Files"
    strSYSDIR = "System32"
End If       
' Set windows directory
strWIN = objWshShell.ExpandEnvironmentStrings("%windir%")
' Set the current directory
strCurrentDir = objFSO.GetParentFolderName(Wscript.ScriptFullName)
' Set computer name
strCompName = objWshShell.ExpandEnvironmentStrings("%computername%")
'/// Main script
    '/// Install via .msi & capture exit code
    'intExitCode = objWshShell.Run("msiexec.exe /i """ & strCurrentDir & "\package.msi""" & " TRANSFORMS=""" & strCurrentDir & _
    '    "\transform.mst"" ALLUSERS=1 Reboot=ReallySuppress /qn", 8, True)
    'wscript.quit(intExitCode)
    '****RUN COMMANDS HERE****
    ' Create folder structure if it doesn't exist already   
    strFullPath = "c:\Windows\Sun\Java\Deployment" '
    ' How many levels are there in the path?
    nLevel = 0
    strParentPath = strFullPath
    Do Until strParentPath = ""
        strParentPath = objFSO.GetParentFolderName(strParentPath)
        nLevel = nLevel + 1
    Loop
    For iLevel = 1 To nLevel
        ' Figure out path for directory at level iLevel
        strParentPath = strFullPath
        For j = 1 To nLevel - iLevel
            strParentPath = objFSO.GetParentFolderName(strParentPath)
          Next
    ' Does this directory exist? If not, create it.
        If objFSO.FolderExists(strParentPath) = False Then
            Set newFolder = objFSO.CreateFolder(strParentPath)
        End If
    Next
    ' Kill running processes
    objWshShell.Run "taskkill /F /IM iexplore.exe", 8, True
    objWshShell.Run "taskkill /F /IM firefox.exe", 8, True
    objWshShell.Run "taskkill /F /IM chrome.exe", 8, True
    objWshShell.Run "taskkill /F /IM javaw.exe", 8, True
    objWshShell.Run "taskkill /F /IM java.exe", 8, True
    objWshShell.Run "taskkill /F /IM jqs.exe", 8, True
    objWshShell.Run "taskkill /F /IM jusched.exe", 8, True
    ' Copy deployment files
    objFSO.CopyFile strCurrentDir & "\deployment.config", "c:\Windows\Sun\Java\Deployment\", True
    objFSO.CopyFile strCurrentDir & "\deployment.properties", "c:\Windows\Sun\Java\Deployment\", True
    ' Disable UAC
'    If bolIsWin8 Or bolIsWin81 = True Then
'        objWshShell.Run "reg.exe ADD HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System /v PromptOnSecureDesktop /t REG_DWORD /d 0 /f", 8, True
'        objWshShell.Run "reg.exe ADD HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System /v EnableLUA /t REG_DWORD /d 0 /f", 8, True
'        objWshShell.Run "reg.exe ADD HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System /v ConsentPromptBehaviorAdmin /t REG_DWORD /d 0 /f", 8, True
'    End If
    ' Install application
    intExitCode = objWshShell.Run("msiexec.exe /i """ & strCurrentDir & "\jre1.7.0_51.msi"" IEXPLORER=1 AUTOUPDATECHECK=0 JAVAUPDATE=0 JU=0 WEB_JAVA=1 ALLUSERS=1 Reboot=ReallySuppress /qn", 8, True)
    ' Enable UAC
'    If bolIsWin8 Or bolIsWin81 = True Then
'        objWshShell.Run "reg.exe ADD HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System /v PromptOnSecureDesktop /t REG_DWORD /d 1 /f", 8, True
'        objWshShell.Run "reg.exe ADD HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System /v EnableLUA /t REG_DWORD /d 1 /f", 8, True
'        objWshShell.Run "reg.exe ADD HKLM\SOFTWARE\Microsoft\Windows\CurrentVersion\Policies\System /v ConsentPromptBehaviorAdmin /t REG_DWORD /d 5 /f", 8, True
'    End If   
    wscript.quit(intExitCode)
    '/// Install via .exe on network
    'objWshShell.Run """" & strCurrentDir & "\Setup.exe"" -s -sms -f1""" & strCurrentDir & _
    '    "\setup.iss"" -f2""" & strWIN & "\Temp\Install-app.txt""", 8, True
    ' Need to turn off the open file security warning first
    Set objEnv = objWshShell.Environment("PROCESS")
    objEnv("SEE_MASK_NOZONECHECKS") = 1
'    intExitCode = objWshShell.Run("""" & strCurrentDir & "\jre-7u45-windows-i586.exe"" /s /v""/norestart " & _
'        "TRANSFORMS=""" & strCurrentDir & "\Tribe-jre7.mst""""", 8, True)
'    WScript.Quit(intExitCode)
    '****RUN COMMANDS HERE****
    ' Then turn it back on
    objEnv.Remove("SEE_MASK_NOZONECHECKS")
'/// Additional functions
Help on this issue would be much appreciated!

Answer 1

It turns out that this is actually a problem with Kronos Workforce Central.  We had the "site.java.plugin.CLSID.familyVersion" setting in that application set to "clsid:CAFEEFAC-0016-0000-FFFF-ABCDEFFEDCBA", which is the Java CLSID for Java 6.  After updating this value to "clsid:8AD9C840-044E-11D1-B3E9-00805F499D93" (the Java universal CLSID), this problem did not occur upon the automatic upgrade of Java.
We have both Java 6 and Java 7 in our environment, and did during our Kronos implementation, so I don't know why we were using the Java 6 CLSID in the first place.
Case closed!