I feel your pain! I have just gone thru this with my MacBook. I am not an expert and tried a number of things and their is probably a better way, but I inserted the Snow Leopard disk that came with the computer. When I started I pressed shift, control, option, p and r. I held them for a bit and finally it broke loose. A window came open to choose language and then openned utilities to repair disk. It said the hard drive was fine. I lost my files from my email and documents I had saved. I also lost Photoshop CS5, and other programs I had to re-register to run them. It has been a major pain as all my passwords and registration information was in files in my email. When I went to my external hard drive to recover things somehow it was not working, probably my ignorance about it.
I have also read that you can use the original disk and press option c when it starts up.
Try using Disk Utility to do a Disk Repair, as shown in this link, while booted up on your install disk.
You could have some directory corruption. Let us know what errors Disk Repair reports and if DU was able to repair them. This could just be a start in repairs and you may need a better utility to finish the job.
Then Repair Permissions.
No need to report any Permissions errors........we all get them.