Are you using Microsoft WHS 2011? It is known that the WHS Mac client, also called LaunchPad.app, can override the Lion version of LaunchPad.app.
If that's the case, you need to first uninstall the MS launchpad, then open up lion installer package to reinstall Essentials package, that'll get your launchpad icon back.
You say you did an in-place upgrade so you don't have the installer package? Then you'll have to create a new volume, install snow leopart, upgrade to 10.6.8, download Lion from App store again, but DO NOT upgrade it yet, instead follow this instruction:
http://osxdaily.com/2011/06/08/create-burn-bootable-mac-os-x-lion-install-disc/