I cloned a drive on the Mac Mini and when the clone started up everything looked in order. However, some apps were giving warnings or dumping when they started.
Twitter for Mac would ask for credentials and then fail.
MS Office 2011 kept giving a warning about the database.
Firefox was missing a profile.
Permissions seemed to be the culprit and then I ran across this forum thread. http://support.mozilla.org/my/questions/785562
The fix was as easy as:
Run this command in terminal from your home directory
sudo chown -R `id -un`:`id -gn` ~