Upon creating or updating a record in Rally, Portfolio items are ordered based on their corresponding rank in Aha! which is determined by their sort order in the Features -> Board view. This is done by using the rankAbove/rankBelow parameter in Rally.
Changes to the rank in Rally are not reflected back into Aha! The problem that is introduced is that Engineering will sometimes need to change the order based on feature synergies or other considerations. However, if a feature is updated in Aha! and re-synced with Rally, it ends up resorting the Features in Rally back to the same original ranked order, undoing Engineering's changes.