This has been going on since approximately the first week of July 2011, but I finally paid attention and figured it out. When the user selects a conditional field which reveals additional fields and the user enters information into those additional fields, the email notification is NOT including the additional fields in the notification.
For example, the user enters their application with name, address, etc. and if they choose the "Family" option then several additional fields are displayed so they can enter additional family names if desired. When they enter additional family names they are not being included in the email notification.
The information that the user entered into the additional fields exists in the entry, but is not being included in the email notification. I'm using {all_fields} - which I've been using all the time. It used to work properly, and I haven't changed anything for months.
Running WP 3.2.1 with Thesis 1.8 and Gravity Forms 1.5.2.8 (and Gravity Forms Paypal add-on 1.2.3). I haven't touched Thesis in months, but I generally upgrade WP and Gravity Forms shortly after an upgrade is available.