Seems like a crazy feature many would not want. Wonder if there might be a preferences setting somewhere to disable it?

I agree. This sounds more like a bug than a feature. Obviously you might still need to access this register or include this account in reports come tax time...
But I certainly wouldn't appreciate this automatic house keeping of accounts.

In Q 2012 Premier:

Tools> Account List> Select all accounts tab on left if you don't see the account you wish to work with> Click Edit button next to account> Select Display Options tab> Make your selections in the Hide or Show Accounts section> Click OK.

Kurt