For what it is worth MacPilot does not list any hidden iTunes preference that would appear to cause this.
Belated recall: I did see something like this on a friend's iMac a month or so back. In her case it turned out she had been interrupted while setting up or changing something in her ITMS account. When she launched iTunes it would immediately go to the ITMS to complete the setup. Finishing the setup "fixed" the problem.
I don't know if this will help or not, but maybe it will give you some ideas.