3G High CPU utilization when waking

Recently gave my iPhone 3G to my wife, restored it to a new phone, then synced it with her information, music, applications, etc. She previously had used an iPod touch, and basically was trying to upgrade her to an iPhone.
The phone worked fine when I had it. I only had a short time with this specific phone as it was replaced under Apple Care about a week and a half before turning it over.
Now it pretty consistently is unresponsive when trying to wake it. By bringing up the System Activity Monitor App as soon as possible after powering it up, and leaving that app active when putting it to sleep I can see that the CPU gets slammed for a while during initial startup and has a significant period of very high CPU when waking. At this point I believe the cause of the unresponsive behavior is that the CPU is maxed out doing something.
I've compared the running processes to an iPhone 3Gs and they were identical except the 3G was missing the MobileMusicPlaye until I brought up the iPod on that phone.
There are 2 things about the initial setup of this phone for my wife that are causing me some concern;
1) When first connected to iTunes after the Factory Reset I was prompted to restore an older backup than the iPod Touch one I took right before the swap. I didn't realize it at the time and accepted that restore.
2) I was prompted to upgrade and followed through with an upgrade to 3.1.2 after the Factory Reset even though the phone was at 3.1.2 before the swap.
At this point I'm thinking about doing another Factory reset and set it up by sync only (no restore) but not looking forward to the time investment that will take.
Any ideas on where the high CPU utilization is coming from on wake? Is that a reasonable theory that the high CPU is causing it to be unresponsive when first woken up.
Any other insight from others that have been through this?

I ended up restoring the 3G phone to Factory settings and then sync'ing the desired information / applications onto it (did not restore the previous backup). The behavior is improved but this phone does seem to get bogged down when waking (observing high CPU utilization when monitoring with System Activity Monitor and experiencing sluggish / jerky response to user actions with no applications or just Mail running). The periods of non-responsiveness are not as long or as severe at this point, but still noticeable.
I'm at a loss since under the conditions I'm observing this there is nothing but Apple software running on the device (behavior is present with or without SAM showing me the CPU utilization). I'm a little suspicious that it might have something to do with re-establishing the WiFi connection, but it seems to continue for a bit after the WiFi icon appears in the status bar.
I'm probably going to make a genius appointment to see if they have any other ideas.

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