Problem After iTunes Update Installed

Question

Software Updates did its automatic check and I noticed the window on the desktop that said there was an update.  I looked at the details and I thought it said itunes update 10.6.3.  I read the details and installed it.  After it installed, I restarted the computer and befor the aple appeared but there was still the gray screen I did NOT hear the tone.  After about 30 seconds the apple appeared and the gear and it booted to the desktop.
I looked at the version of iTunes by going to About iTunes and the moving box said (althought it was really small this time) but I checked it again and it said 10.6 (4.0).  However, I thought when the Updater said there was a newer version of iTunes, I thought it said version 10.6.3, with no paranthesis.
I restarted the MacBook Pro again, and still there was no tone but the gray window was present for about 10 secs then the Apple, and it booted to the desktop.  I thought I should get a tone so I shut the MacBook Pro down and pressed the Power button to boot up in Safe Mode, but I did not hear the tone so I did not press the Shift key.  I checked the version of iTunes that was installed (assuming a newer version was installed) and it is 10.6 (4.0).
I tured the computer off and tried to do a SMC Reset.  I turned the MacBook Pro of left for a couple hours, came back, plugged the MagSafe Adapter in and tried to boot up the computer, no tone heard, the gray screen appeared for about 20 secs, then the Apple, then the gear and it booted to the desktop.
Something has been recently occuring.  when I plug in the MagSafe Adapter initially, next to the battery up in the menu next to the Bluetooth icon it says "Not charging" but after about 5 secs it has the charging sign in the middle of the battery.  Not sure if this is related or what.  I tried to do an SMC Reset when I saw this "Not Charging" when I plugged in the Mag Safe  but it did not change anything as far as when I plug in the Mag Safe Adapter it still initially says "Not Charging" for about 5 secs and then it goes away.
I am concerned what to do about hearing no tone and the version of iTunes I thought it said it was going to install but when I checked About iTunes it says 10.6 (4.0)
any help in this matter.  I am not the best when it comes to computer knowledge.
thanks

Answer 1

Your explanations have clarified some things (including one misconception I had from not reading your post carefully enough -- I thought you had "hard shut down" by holding down the power button, no in rereading your post, it sounds like you did not do that but rather shut down in an orderly way, that was my misconception).
I too was not aware of the Magsafe Power Supply issues, but it sounds like you would be well off to use that settlement check to obtain a new one. Hopefully that will resolve the charging issues you saw. I work somewhere where there are literally hundreds of Macbook Pro and Air laptops, all with these Magsafe adaptors, and I haven't seen any such complaints, but perhaps yours was part of a bad batch, it sounds like you're not the only one. (I have seen such chargers just wear out after 4-5 years, but then they just stop working altogether, versus the "charging/not charging" business you were seeing.)
I am going to surmise that none of the Magsafe issues have anything to do with iTunes because iTunes is just an application that is not related to the way the laptop charges. I suspect it is a coincidence that the iTunes update happened around the same time. The Magsafe behaviors probably would have manifested themselves even if you had not done the update.
Is your sound working in iTunes? Do you still not have boot up sound? If the answer to both of these questions is yes, you may want to read this Apple article  http://support.apple.com/kb/ht1379  and consider doing a reset of your PRAM and/or NVRAM. I noticed that PRAM does control some sound settings and "attention tones" of the computer (which might include a startup tone perhaps).  Something to consider, it's hard to offer advice in these cases without being there in person to observe things. Good luck with all this.
Before you do any resets on PRAM or NVRAM, do re-check your sound settings to confirm that the mute box is not checked. When my Macbook Pro mute box is checked, I get no startup chime also. You might consider checking the mute box, restaring, then unchecking it again just to see if that matters. One last thing -- some other posts in the Discussions involved Macs without a startup chime and people got their chime back after disconnecting or fixing a peripheral that was plugged in via USB or Firewire. I don't understand why that would be, but that is what they reported -- something else for you to consider.