One more thing - - which I seem to be recommending to everyone: try rebuilding the startup disk directory with Alsoft's DiskWarrior (starting from the DiskWarrior CD). If you don't have DiskWarrior, I suggest acquiring it ASAP - - as it is THE essential disk utility for Macs. For me, it has fixed problems that no other software even detected - - although they were, in actual practice, obvious anomalies.
I found DiskWarrior especially useful after installing the 10.4.9 update. After updating from Altiverb 5 to Altiverb 6, Logic refused to "see" Altiverb 6 and insisted that Altiverb 5 was "missing." After installing Izotope Ozone, it asked for its licensing code every time I opened it - although I had entered the code and registered the software. After installing OS 10.4.9, the first opening of one instance of an empty Vienna Instruments instance took over 6 minutes.
Rebuilding the directory with DiskWarrior fixed every one of these problems. Sometimes it reported a couple of minor errors, but, on some occasions, it just stated that "all errors, if any, have been fixed." Whether or not it reported a specific error, the anomalies simply ceased to exist: Logic immediately recognized Altiverb 6, Ozone opened without requiring me to re-enter the authorization code, and a single instance of an empty VI plugin loaded in 1 minute and 10 seconds.
One other thing, installing the OS 10.4.9 update can corrupt some software. In my case, it corrupted MS/Office so that the Equation Editor was no longer accessible. The cure was uninstalling and then re-installing MS/Office Not only did Equation Editor work again, but all elements of the application now function at about twice their previous speed.