If iPhoto didn't save the changes or you synced before it did somehow (if you have them in an album, check to see if the rotation is only in the album, not the library, or vice versa) I would suggest doing that check, quitting iPhoto and then re-syncing the device. If that doesn't work, unsync the photo's through iTunes (plug in your Touch and head to the Photo tab and uncheck that particular album or entire library if you sync everything), and then resync everything after they are gone.
Maybe something had a hiccup in the process and the photos were transferred over incorrectly, and since they are already on the Touch they aren't updating properly when re-synced.