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Here is a walk through on deploying Office as an Application: http://gallery.technet.microsoft.com/office/How-to-Deploying-Office-0f954e7f and here is a guide on deploying an exe as an Application: http://tjindarr.wordpress.com/2012/03/30/deploy-exe-files-as-a-msu-deployment-type/ I use both in our environment for Office 2010/2013 and Firefox respectively.

Sorry to revive an old thread, but I found this on Google and have been troubleshooting this for a few days now. I found a solution to the original problem and wanted to share in case someone else stumbles upon this in the future. When installing the Remedy via SCCM (2012 SP1 in my case), there are 2 things that are important. The working directory has to be the folder ABOVE the Disk1 folder. Remedy requires the folder be called Disk1 and since SCCM copies the files to a cache, that link will break unless we copy up the entire Disk1 folder. The Options.txt file has to be the full path even if the file is in the working directory. I created an application with the contents contained in \\Server_Name\Folder_Name\ and ran the install command Disk1\setup.cmd -i silent -DOPTIONS_FILE="\\Server_Name\Folder_Name\Disk1\Options.txt" *Technically this will still fail because the detection method kicks off write after the setup.cmd script runs, but if you wait until the install finishes look in the Program Files or Start Menu, it is installed successfully.