Apple has specified that if the preferences are not found that the application should create a new version of them. If their own developers are doing this, well...they should be shot with rubber bands (which they probably have happen anyway).
I have had problems with System Profiler from time to time as far as it would display incorrect connections...FireWire drive on SCSI card, etc. but that's all been corrected.
I saw that you have another thread open now. Have you repaired permissions?