Files Missing From Time Machine Backup

I had a system crash and I'm trying to move the files from my time machine backup onto my new computer.
The problem is that many of my files, which I know where on my desktop in folder at the time of the backups, seem to be missing. I can find the folder, but about three quarters of the files from it are gone. The ones that are in it appear to be mostly newer files that I had created not long before the last backups and the crash. As far as I go back, the files seem to be missing.
Anyone know what might be going on?
Does it have to do with which user I'm logged in as? Would that change what files I can see?
Any suggestions?
Thanks.

Thanks for the comment. I did use the Migration Asst. to move her data and most did move, but key information, like the Safari Bookmarks, the addresses in the Address Book, and every file in the Documents folder were all missing. I finally called Apple and the tech there solved the problem. The source of the problem is that when she registered the new Mac mini, she used a slightly different User name, which then made it impossible for the new Mini to communicate with the external Backup data. The tech walked me through a multiple step process that involved adding a suffix to the original user name and so on, which has made available all the original data on the new mini.
This is the second time in the last few years that a change in the administrator user name has created an enormous problem. While Apple notes that this user name is important, there should be a more thorough explanation of how it functions and the serious consequences that can occur if is not husbanded properly.

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