Some files hidden after restore

So I changed computers twice in the past three months, and each switch was done using my TimeMachine backup to setup the new computer. Now some of the folders in my home folder are hidden. I am not referring to standard hidden files with a period at the front of the name, but folders I created and used in the normal use of the computer. It is more of a "Windows" style of hidden, and it may be related to the fact I am on an Active Directory network.
My current work around is to just show all hidden files, but I would rather have things work as they should. Any copy I make of the hidden files maintains the hidden characteristic. Most any idea is welcome, but don't suggest I speak to the network administrator here at the school where I work since that is me.

Launch /Applications/Utilities/Terminal. Cop-y/paste this line of code at the prompt in Terminal...
*sudo chflags nohidden*
Then drag the file or folder you want unhidden to your Terminal window.
It will now show the path to the item.
Press Return.
-mj

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