As esXXI says, this sounds like a general problem with your OS, not a specific ShapeShifter issue. Gerrit's anecdote about the OS suddenly "losing" the home folder or the preferences folder seems to be a common failure mode for OS X. I'd imagine that rebooting after installing ShapeShifter exposed an existing problem.
An Archive and Install is the easiest, but most time-consuming fix. If instead, you'd like to try disabling ShapeShifter to see whether it's responsible, do the following:
Another option is to use the Accounts preference pane to create a new Administrative user. You can log in as the new user and use that to see whether your original user's home directory was renamed, or whether its Library or Preferences folder were renamed, or something along those lines.
An Archive and Install is the easiest, but most time-consuming fix. If instead, you'd like to try disabling ShapeShifter to see whether it's responsible, do the following:
- Choose System Preferences from the Apple menu
- Choose the Application Enhancer preference pane
- Choose the Application Enhancer tab
- Press the "Disable Temporarily" button
- Quit System Preferences
- Choose Restart from the Apple menu
Another option is to use the Accounts preference pane to create a new Administrative user. You can log in as the new user and use that to see whether your original user's home directory was renamed, or whether its Library or Preferences folder were renamed, or something along those lines.