Hi JGS28,
Here's an article that explains the 90 day restriction with changing the association of Apple IDs with computer and devices.
iTunes Store: Associating a device or computer to your Apple ID
http://support.apple.com/kb/HT4627
…Once a device or computer is associated with your Apple ID, you cannot associate that device or computer with another Apple ID for 90 days. You can view which devices or computers are currently associated with your Apple ID, remove unused devices or computers, and view how many days remain before the devices or computers can be associated with a different Apple ID from the Account Information page in iTunes on your computer:
Open iTunes.
Sign in to your Apple ID by choosing Store > Sign In from the iTunes menu.
Choose Store > View My Account from the iTunes menu.
From the Account Information screen, click Manage Devices.
Next to each device or computer name, you will be able to see when each device or computer was associated with your Apple ID. You will also be able to track how many days remain before your associated devices or computers can be associated with a different Apple ID.
It sounds like your wife's iPhone is working correctly.
Thank you for visiting Apple Support Communities.
Nubz
