Unrepairable "different" Permissions After Updating iTunes

Hello -
First, I need to confess that I am not an Apple computer guru. However, up until today, I've never experienced any major problems with either of my two Mac computers.
Ugh. . .
I updated both the iTunes and Front Row programs on my MacBook Pro today. I did what I usually do after performing any major update or upgrade, I repair the permissions via the Disk Utility program. This utility almost always repairs any of the changes that may have occurred during the updating/upgrading process. It did not work this time, unfortunately.
I am unable to repair the dozen or so differing permissions that the Disk Utility tells me exists. I click the "Repair Disk Permissions" and when it's finished it tells me, "Permissions repair complete". I, then, click "Verify Disk Permissions" and receive the same messages as before; that there are many differing permissions.
So. . . here are my questions:
1) Will this apparent problem of differing permissions effect the overall performance and stability of my computer in any way? (I use the MacBook Pro mainly as a slave computer for instrumental software plug-ins for sequencing projects.) (By the way. . . "So far, so good". I haven't noticed any problems, YET, when loading up my Kontakt 2 and Kontakt 2 Player instrumental software programs.)
2) Will this apparent problem leave my MacBook Pro vulnerable to future problems (like future program updates, computer viruses, etc)?
3) Is there any way to fix this apparent problem??
Thankfully, I did NOT upgrade the iTunes on the larger MacPro computer which houses main audio and video editing software programs. In fact, I very rarely use the iTunes program. The only reason I keep it on the MacBook Pro is because my wife owns an iPod device. But she keeps her iPod hooked up to her aging yet dependable Dell laptop computer. (I don't think she even updated her Windows version of iTunes yet! LOL!) Silly, silly me for updating a program I don't even use. Now, I humbly wish to fix this problem before it get worse. I use the MacBook Pro all the time for my music-sequencing projects (as a slave computer to my MacPro).
Thank you in advance. . .
Embarrassed. . . . and GRATEFUL for any solutions to this apparent problem. . .
Ted

Thank You!!
I read the entire link that you supplied. Very Informative!! It also relieved my anxiety quite a bit!
Again, thank you!
Ted

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