I've been seeing an issue with Casper Imaging. As part of a nuke and pave imaging workflow, I created a package from the app CreateUserPkg that creates my primary admin account. I was using ID=499. However, on first boot after Casper Imaging I kept getting a dialog box stating "OS X needs to repair your Library to run applications. Type your password to alow this." I would find the home directory was missing important folders such as Desktop, Pictures, Music, Movies and what there was of the home directory had incorrect permissions. I would end up booting in single-user mode, mounting the file system for writing and deleting the home directory to force a clean creation on next login after rebooting.
After changing the account ID to 501, the first "normal" ID in OS X, all is well. The only thing I modified in the admin account creation package was the account ID. The app chose a new UUID, of course, and I didn't bother to make it the same as it doesn't matter.
Anyone else seeing this problem? The OS I am imaging with is 10.9.5 on a Mac Pro 2013 and I am using Casper 9.73.
It has become such a pain to hide the admin account that I don't bother anymore. Just wanted to document the problem in case anyone else has come across it.