Since Ubuntu 9.04 was released with a newer version of Java, we just had to try ChemDoodle on the upgraded OS. We all agree that ChemDoodle on Ubuntu 9.04 is faster than on previous versions of the OS and several Java glitches have been repaired, most notably, the missing borders around comboboxes.
UPDATE: ChemDoodle 2 was released on 5/27/09.
Warnings aside, if you can safely and successfully install Ubuntu 9.04, we recommend it. ChemDoodle’s performance is definitely improved with this upgrade.