The issue is not related to ISE per say.
When a user changes his/her password the popup appears as per my original post. This popup however dissapears 1-2 seconds later. Please keep in mind that ISE sends the authentication requests to an external identity source.
I am sure anyone else who setup 802.1x would get this issue where the popup is way to fast to re-enter your credetials after the password change. I added the 2nd screenshot on showing that you can enable it to automatically use your domain credentials. This however is not always feasable to have it automattically use the users domain credentials.