Corrupted Mac OS X Install disk?

I have an early 2010 MacBook which came with Snow Leopard. I had trouble with the permissions for quite awhile; every time I did a software update I would have trouble booting up and would get stuck on the start up screen. Disk Utility and fsck sometimes helped. Last week I could not get anything to work and could not boot it up at all so I took it to the Geniuses at my Mac Store and they said the HD was fine, but obv the software had issues so they did a free Archive & Install. Everything was fine after that.
Then I bought a new HD to use as a back up, and after I got home I realized it was bigger and faster than the one already in my MacBook so I decided to switch them out. Then I installed Snow Leopard from my Mac OS X Install disk onto the new HD. Now I have software issues and permissions issues again. When I do Disk Utility and try to repair permissions it just keeps saying the same permissions are corrupted over and over, and tells me that some of them will not be repaired.
Does this mean that my Mac OSX Install disk is corrupted? How would I go about getting a new one so I can start over clean again without problems? If I take my MacBook back to the Geniuses, I don't know if they will do an A&I for free again, and also, if I ever need the OS X Install disk for future, I'd like to have one that's not faulty.
Any thoughts? Thanks!

Thanks Lumnos, I appreciate your thoughts and your time in responding.
I decided to reformat and erase the hard drive and reinstall Snow Leopard just to see what would happen. So I started up the computer to Disk Utility using the OS X Install DVD. I clicked on the name of the HD and then clicked "erase". When that was done I went back to the Snow Leopard Installation screen and went through that process. This is all on the HD that I just bought 2 days ago, BTW.
I know you said the iTunes thing is probably unrelated to any permissions problem, but I wanted to see what it looked like after wiping the HD. So after the OS was installed, the first thing I did after start up was open iTunes. It still does not display the Store or recognize my devices.
Then I rebooted into Disk Utility like you suggested. I verified the disk. It said "Macintosh HD appears to be OK" without any messages about having modified anything.
Then I verified permissions. All it said was something like "Verification of permissions is complete" and didn't give any other report, no error messages, nothing, except that it was complete.
Then I tried repairing permissions, and it did the same thing. Said it was complete without any other messages.
So I guess the permissions and the disk are fine?
Any thoughts on what to do about iTunes? I don't think updating the iTunes software will change anything, as all my software was updated prior to posting this discussion, and I was having the same problem.

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