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You can try a clean install to repair Ulysses. As you've previously used an older version, I think you still have an old serial number (less than 7 digits long) which only works for Ulysses 1.x. You can get the last 1.x release Ulysses 1.6r2 at http://www.the-soulmen.com/pub/ulysses/history/Ulysses%201.6.dmg . Just delete the old Ulysses.app from your Applications folder and replace it with the downloaded copy.
You can also give Ulysses 2.0 a try which you can get at http://www.the-soulmen.com/ulysses/ . It's a 60 day trial and you can buy the upgrade at the reduced upgrade price of 24.99 EUR at http://www.the-soulmen.com/shop/?key=ULYS .