For TimeQuest to report phase shift change due to changes in DQS delay chain settings, you also have to change the DQS phase shift setting in the Megawizard™ Plug in Manager for ALTDQ_DQS.
For example, in Stratix® IV device, if your frequency mode is 1, you will get phase shift options of 30, 60, 90 or 120; If you choose "Number of stages in dqs_delay_chain" of 3, you will get 90 degree phase shift and if you choose 1, you will get 30 degrees phase shift. TimeQuest will only show this change if you also change the "DQS Phase Shift" option under "Advanced delay chain option" on the second page of the Megawizard Plug in Manager GUI from 3000 to 9000 (3000 gives you 30 degrees phase shift and 9000 gives 90 degrees).