Sorry, but I still haven't gotten the problem figured out. If anyone reading this has experience with Windows Installer and/or WiX, I'd love to hear from you!

With Alarm Clock 0.7.0 there were some changes made to the Windows Installer package which have lead to the disappearance of the desktop and Start Menu shortcuts for the program. I'm currently working on the problem and with any luck, 0.7.1 should be available tomorrow with the installer problem ironed out. There won't be any code changes for the new version, it'll simply be fixing the installer package. Sorry folks!