IPhone not Working with iTunes on New iMac

I recently upgraded a family member's iMac from an early Intel iMac to a new i5 iMac. Both the old and the new were running 10.6.4 and had iTunes 9.2.1.
I used the simple transfer functionality when setting up the new iMac to transfer everything over from the old iMac
When I loaded up iTunes on the new iMac and connected the iPhone (3GS, iOS 4.0.2), nothing happened. I checked System Profiler and it was there.
After trying a couple times, restarting, etc, I followed the instructions here to entirely remove and reinstall iTunes and its files from the new iMac: http://support.apple.com/kb/ht1224
(I did everything, including the "Additionally..." instructions at the bottom).
This did the trick - The iPhone was recognized by iTunes. However, the next time I restarted the iMac everything went back to the old (no iPhone recognition by iTunes).
Any advice on what I might be missing?
Message was edited by: Kai Brinker

It seems I only need to reinstall iTunes, not delete everything first, to get iTunes to recognize the iPhone until restart.
What in the restart process could cause this to go away?

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