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MSI install using \system32 directory instead of ccmcache\"x" directory

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I cannot recall if this has always been happening or not, but I've got a big project here at work to bring in +150 softwares to ConfigMgr Application Management. Using the Create Application Wizard and selecting Windows Installer *.msi file, it is auto filling the Install Program line with, for example, 

msiexec /i "AdbeRdr1010_en_US.msi" /q

I would like to add the patch and a transform, which if ran locally I could use:

msiexec /i "AdbeRdr1010_en_US.msi" PATCH="AdbeRdrUpd1017.msp" TRANSFORMS="GA_Adobe_Reader.mst" /qn

But when using this with ConfigMgr it fails. I thought at first it was failing because it was switching the working directory to C:\Windows\System32 because that's where msiexec.exe exist and in the AppEnforce log it shows:

Executing Command line: "C:\Windows\system32\msiexec.exe" /i "AdbeRdr1010_en_US.msi" PATCH="AdbeRdrUpd1017.msp" TRANSFORMS="GA_Adobe_Reader.mst" /qn 

But I can run ReaderXI with a transform using:

Executing Command line: "C:\Windows\system32\msiexec.exe" /i "AcroRead.msi" TRANSFORMS="Adobe_AdobeReaderXI_11.0.02_ENG_R1.mst" EULA_ACCEPT=YES /qn 

and it completes successful. THe only differnce I see is the use of PATCH="AdbeRdrUpd1017.msp"

I have tried using %~dp0 before the msp but it still fails. 

I would like to keep everything clean so I'd rather not have the main install then a second application package to apply the patch. I know I could also run the command from a batch/cmd file, but it seems silly to call a batch with a single line that seems like I should be able to do all this natively from the single line in the Application properties. 

Thanks



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