Is this a brand-new MacBook Pro? If so, it should be running Mac OS X 10.7 (Lion), which does not come with install disks. To reinstall, you simply hold down command-R at startup to boot into recovery mode. From there, you would erase the hard drive with Disk Utility and reinstall the system. Note that you'll need a good internet connection, as it will need to download a lot of data. (Not sure exactly how much, but the installer downloaded from the App Store for older machines that didn't come with Lion is 3.76 GB.)
There shouldn't be any risk to doing that if all the data is stored elsewhere. And don't try to use Migration Assistant, use the Setup Assistant that asks about importing data from an old machine the first time you boot the new system.
Follow Thomas Reed's advice with Lion Recovery and then simply use the same partition drive name and user name on the new machine when going through the setiup.
Then instead of using Setup Assistant which asks to transfer from another Mac, just skip that part.
Software Update, then install programs from fresh sources and finally transfer the contents of the user file folders (Music, Pictures, Documents etc) of the old Mac into their respective folders on the new Mac. (you can use a external drive or Firewire Target Disk Mode for this)
As long as the partition name is the same and the user name is the same, the pathnames match in iTunes and you don't get exclamation points to missing songs as their locations don't appear to have moved.
Also because you installed OS X first and updated, then installed programs, then lastly user files which change often, your boot drive remains optimized for maximum performance longer than if you used other methods.
Lots of people complain their computers slow down after using migration and or setup assistant. So by following my steps you avoid that slowdown.
Also by installing programs fresh and transferring files manually, you avoid any pitfalls with certain software that doesn't run correctly on OS X Lion, namely Rosetta programs and anti-malware/root level installed programs which also could be the cause of your issues.
Migration and Setup Assistant blindly copies, there is no intelligence as it's impossible to catagorize all third party software accuratly so by installing what programs you use from fresh sources you ensure it works for Lion.
I am running into the exact same problem as you. I would like to start from scratch as I have no new files, but I am concerned that in order to get the programs I want from iLife, namely iPhoto and iMovie, the help instructions say that I will have to buy them from the App store for $50! Is this the way you understand it? I think this looks like another Apple scam!