I want to second Rino's recommendation of Alsoft's DiskWarrior. In my case, on quite a number of occasions, running DiskWarrior solved For exampleotherwise inexplicable problems that Apple's Disk Utility did not see and could not be corrected by "repairing persmissions."
On one occasion Diskwarrior saved a disk that evey other disk utility reported beyond repair. Rebuilding the directory of this disk took over 12 hours (normally DiskWarrior takes about 15 minutes to rebuild the directory of a 250GB disk), but saved all the data on that disk. One more example: recently, I installed a new version of Altiverb (v.6) but Logic did not recognize its presence. No amount of trashing preferences, repairing permissions or running Apple's Disk Utility changed this behavior. However, rebuilding the directory of the startup disk with DiskWarrior resulted in an immediate cure. Diskwarrior, unfortunately, does not always give a full accounting of what it fixed - - in this case its report stated that it had found problems with custom icon flags affecting four fonts associated with Finale and made no mention of Logic or Altiverb. Nonetheless it fixed something that made it possible for Logic to recognize Altiverb. DiskWarrior is now available in a Universal Binary version that works on Intel Macs as well as PPCs.
On one occasion Diskwarrior saved a disk that evey other disk utility reported beyond repair. Rebuilding the directory of this disk took over 12 hours (normally DiskWarrior takes about 15 minutes to rebuild the directory of a 250GB disk), but saved all the data on that disk. One more example: recently, I installed a new version of Altiverb (v.6) but Logic did not recognize its presence. No amount of trashing preferences, repairing permissions or running Apple's Disk Utility changed this behavior. However, rebuilding the directory of the startup disk with DiskWarrior resulted in an immediate cure. Diskwarrior, unfortunately, does not always give a full accounting of what it fixed - - in this case its report stated that it had found problems with custom icon flags affecting four fonts associated with Finale and made no mention of Logic or Altiverb. Nonetheless it fixed something that made it possible for Logic to recognize Altiverb. DiskWarrior is now available in a Universal Binary version that works on Intel Macs as well as PPCs.