Here was my winning solution to deploy Salesforce.com Chatter Desktop. Download the Adobe AIR EXE, and the AIR package from Salesforce.com's Desktop Administration of their website. Package them up as a ZIP, and use this as the managed installation:
Override Default Installation, and use this as the full command line:
AdobeAIRInstaller.exe -silent -desktopShortcut -programMenu desktop_mv_3.2.2.air
Don't forget to uncheck Prepend msiexec.exe!
Setup Type: Windows Installer (Delivered as an EXE)
Deployment Method Used: Vendor Provided Command Line (switch driven)