this is what i use when deploying with SCCM 2012.

for Active X:

msiexec /i flash_player_12_active_x.msi /quiet /norestart /log "C:\WIndows\Temp\flashActivX12.log"

For Plugin:

msiexec /i flash_player_12_plugin.msi /quiet /norestart /log "C:\WIndows\Temp\flashPlugin12.log"

If you want to do the installation with the updates feature turned off, do this:

Here are 2 vbs scripts for install and uninstall Adobe Flash Player 12: 

- both scripts are running in silent mode.

- the install script is set the Auto Update - Disabled (-au 2)

install.vbs

 Option Explicit

Dim strScriptPath : strScriptPath = Left(WScript.ScriptFullName, InStrRev(WScript.ScriptFullName, "\")-1)

Dim objWSH
Set objWSH = CreateObject("WScript.Shell")

DisableSecurity()

'Run a exe setup
'================
Dim INSTALL_ACTIVEX_CMD, INSTALL_PLUGIN_CMD

INSTALL_ACTIVEX_CMD = """" & strScriptPath & "\install_flash_player_12_active_x.exe"" -install -au 2" 
INSTALL_PLUGIN_CMD = """" & strScriptPath & "\install_flash_player_12_plugin.exe"" -install -au 2"

objWSH.Run INSTALL_ACTIVEX_CMD,,True
objWSH.Run INSTALL_PLUGIN_CMD,,True

Sub DisableSecurity()
	Dim objEnvProc, objWSH
	Set objWSH = CreateObject("WScript.Shell")
	Set objEnvProc = objWSH.Environment("PROCESS")
	objEnvProc("SEE_MASK_NOZONECHECKS") = 1
End Sub

- the script is installing the Adobe Flash Player 12 ActiveX and the Plugin with Auto Update disabled.

- the DisableSecurity sub is used to disable the security warnigs. 

remove.vbs

 Option Explicit

Dim strScriptPath : strScriptPath = Left(WScript.ScriptFullName, InStrRev(WScript.ScriptFullName, "\")-1)
Dim objWSH
Set objWSH = CreateObject("WScript.Shell")

'Run a exe setup
'================
Dim CMD_Remove_ActiveX, CMD_Remove_Plugin
Dim UninstallCMD, UninstallRegKey

UninstallCMD = GetRegValue("HKEY_LOCAL_MACHINE\SOFTWARE\Macromedia\FlashPlayerActiveX\UninstallerPath")
CMD_Remove_ActiveX = UninstallCMD & " -uninstall"

objWSH.Run CMD_Remove_ActiveX,,True

DeleteFolder("c:\Windows\SysWOW64\Macromed")
DeleteFolder("c:\Windows\System32\Macromed")

Function ExistRegKey(regKey)
    Dim wshShell, str
    Set wshShell = CreateObject("WScript.Shell")
    On Error Resume Next
    str = wshShell.RegRead(regKey)
    If str = "" Then
        ExistRegKey = False
    Else
        ExistRegKey = True
    End If
    Set wshShell = Nothing
End Function

Function GetRegValue(regKey)
    Dim wshShell, str
    Set wshShell = CreateObject("WScript.Shell")
    If ExistRegKey(regKey) Then
        str = wshShell.RegRead(regKey)
        GetRegValue = str
    Else
        GetRegValue = "NOT FOUND"
    End If
    Set wshShell = Nothing
End Function

Function DeleteFolder(strFolderPath)
	Dim objFSO
	
	Set objFSO = CreateObject("Scripting.FileSystemObject")

	If (objFSO.FolderExists (strFolderPath)) Then
		objFSO.DeleteFolder (strFolderPath)
	End if
End Function

- the script is removing the Adobe Flash Player 12 ActiveX and Plugin.

- Both scrips are working with all minor versions of Adobe Flash Player 12

- In order to use the scripts, just copy them in the same folder with install_flash_player_12_active_x.exe and install_flash_player_12_plugin.exe files. 

Important note: these scripts are workin only with exe installers downloaded from Adobe portal: http://www.adobe.com/products/flashplayer/distribution3.html

Rather than faff about with adding files via a transform, just ammend the custom action that does the install (NewCustomAction1) to add -au 2 to the end of the command line.

This generates the mms.cfg file with the following contents:

SilentAutoUpdateEnable=0

AutoUpdateDisable=1

Thanks for the idea packageologist! To elaborate for those like myself still learning,

1. Open the Flash msi file using an editor like orca.

2. Inside Orca, Select CustomAction from Tables on the left pane.

3. Find the "NewCustomAction1" Action on the right pane and find the cell in the "Target" column. The cell it should show -install -msi

4. Double click the cell and add "-au 2" as packageologist mentioned above. The cell should now read "-install -msi -au 2" without the quotes of course.

5. save your modified MSI and you're off and running.