A couple of things....
1. The disambiguation dialog still comes up. We have not removed that capability or functionality, but it has improved. Meaning, if you have duplicates, but they are both the same email address, then there really is not any difference on which one you choose, so we don't bother you with selection, we simply choose the first one and move on. So, if you have duplicates...same display name, but different email addresses in the same address book - the disambiguation dialog will still appear.
2. Search order - why is having the System Address Book first in the list so important? The intent of Frequent Contacts is that not only do you get 'just' the addresses from the SAB that you actually use, but also you should get quicker response and editable entries. Is there some problem you are trying to 'fix' with having the SAB first in the search order? The only one I know of is if the SAB entry gets edited and a new email address is in the SAB, historically this did not always get synchronized to the Frequent Contacts in a timely manner. That is a very very old issue. Not only does synchronization happen more frequently, but it also does not matter. GroupWise's late binding will accurately resolve the email address and deliver as expected. We would be very interested in a duplicatable issue related to this.