I've just discovered the vanishing apps problem, and this was on a new out-of-the-box Mac Mini with Lion 10.7.3.
- Unboxed a brand new Mini, hooked up peripherals, turned on
- When the first time wizard got to the Migrate option I hooked up my old Snow Leopard MBP in target disk mode via Firewire and copied Users (just me), Apps, and Settings
- On the first startup all but two of my apps had successfully migrated. I ran one, Google Chrome, to download the Lion version of an M-Audio driver.
- Did Software Update that returned five updates, no reboot required -- this Mac had just shipped so the OS and bundled apps were almost completely up to date
- Ran App Store to update and install purchased apps
- Disabled the Guest user
- Installed the new M-Audio driver, which required a restart
So, significant points so far -- after running Migration Wizard at least one of my old apps, Chrome, was there, since I was able to run it. Only two were reported as unmigrated. But after rebooting the system for the first time, my Dock applications got an overlaid question mark when I tried to run them. They were no longer in /Applications. From a bash prompt I've searched the file system and found nothing. Fortunately my Application Support is intact so it looks like I didn't lose any data.
The /Applications folder now contained only the apps which had come pre-bundled on the Mac, BUT they still had their App Store updates. Which makes more sense than them somehow reverting. And the one un-migrated app I installed (the M-Audio driver) was still there. But all of the migrated apps were deleted when I rebooted.
So why would a brand new Mac migrate non-bundled applications and then delete them all on the next reboot? Had I known this would happen I would have verified their location and looked at their file attributes. I even tried re-enabling the Guest User in case they were in one of that user's directories.
Honestly, not the best experience to have with a brand new Mac out of the box, even if I didn't lose any personal data (and the old MBP is thoroughly backed up, and this one will be too.) I may try reproducing it by re-running Migration Assistant on the apps, but I can't reproduce whatever the OS's state was when I first started it up.