Casey,

I assume that you mean the Install File(s) setup function? First of all, check the uninstall log to see if the file names are in that log. If this is the case, then something deleted the files AFTER the installation process (e.g. a protection software product). Then check if you have "excluded" Windows Server 2012 in the File conditions tab.

And another quick idea. If the files are in-use and Windows reboots to complete the installation process, under certain circumstances Windows deletes the files. You can try to avoid this by setting the temporary files folder to your installation folder (using the "Set Temporary File Folder..." script function).

Hope this helps a bit.

Friedrich