Boot up from the installation disk to run your disk utilities, you might have been doing it from the utilities of the hard drive itself and that really doesn't free up the hard drive. Check to see if you have at least 10% free hard drive space. You also may have developed some bad blocks or the hard drive may be failing. If the repair and permissions fix does not work from the installation disk, reformat and do a low level format using the "zero data" option, this will eliminate any bad blocks that may have developed. Then backup from the Time Machine and run Disk Utilities from the DVD again.