New, updated, even reinstalled. Must repair many permissions. Only OHuh?

Could someone please explain to me why I had a long list of disk permissions to repair

Continue. First was posted inadvertently.
Nothing on the new Mac Pro except FCP and OSX. Even reinstalled (disk format), because there was a problem with the keyboard. Everything updated. Our internet connection is secure through the Swiss telephone company. We use the computer for nothing except updates.
The list of disk permissions to repair was hundreds long, and included a wide variety of places, like Itunes (haven't even agreed to the contract yet).
We did click yes to a contract while we were running a series of updates on FCP.
Idly curious.

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