Yes, lots of people have issues with 10.3.9 on the G5. The most stable version of Panther seems to be 10.3.8 for the G5s and 10.3.4 for the G4s. If you want to use FCP5 you might consider moving up to Tiger. Until reliability issues are resolved with the FCP5/Panther or Tiger combo I would have a firewire drive with FCP4/Panther 10.3.8 installed and 10.4 Tiger/FCP5 on your main startup drive. A lot of the trouble concerning new software is because recommended install procedures are not being followed by the user. Go to the Apple web site and read about upgrading and make sure you’re doing it the right way.
If you do a search in this forum you’ll also find lots of threads on this topic.
– Don