I was helping out with a customer’s Active Directory migration and a different IT support group used a profile migration tool to help “ease” the transition between domains. But soon after the users started complaining that IE was not allowing them to save passwords. They would get prompted to store the credentials for a website and click yes, but as soon as they closed and reopened IE their stored credentials would disappear. Our suspicion was that the profile migration tool had corrupted the credential store in the registry.
I started a remote session with one of the users, checked the IE password store in the registry (HKEY_CURRENT_USER\Software\Microsoft\Internet Explorer\IntelliForms\Storage2), and saw several of the user’s old entries. In order to allow the user to store passwords again, I had to delete this registry key, reopen IE, and save credentials for a website. Once I clicked “yes” to the prompt to save credentials, the registry key was automatically recreated and the credentials got stored.