More info for anyone who is interested. Deploy.exe does more than run the main msi, it also starts a number of other installs. To completely replicate what Deploy is doing you must take a look at the INI file (my_install.ini).
For example, this is what I am doing with 2007, executed via a VB script.
msi\WindowsInstaller-KB893803-v2-x86.exe /quiet /norestart
support\dotnetfx\dotnetfx.exe /q /c:"install /l /qb"
support\DirectX\DXSETUP.exe /silent
support\mdac_typ.exe /q:a /c:"setup.exe /qnt"
msiexec /i support\aev\SetupDWFViewer.msi REBOOTPROMPT=S /qb!
msiexec /i support\flash\InstallFlashPlayer9ActiveX.msi REBOOTPROMPT=S /qb!
msiexec /i acad.msi TRANSFORMS=my_install.mst REBOOT=Suppress /qb-