Only for new installs, not upgrades from previous installations.
Using wp 3.0 as mu with a new install of ata 3.5.1. So far so good except was having problems with the search box location. After many hours discovered that the download of 3.5.1 I got had active CSS in the CSS Inserts that modified the search box and other stuff. Set it to the default of blank and all worked as expected.
Could also effect other styling so you should check to see if your download has css code inserted.
Also, noticed that a lot of the set-up had non-default values inserted.