I updated the "Surprise" theme for Winterboard today in Cydia, and during it an itunes password prompt came up. Does it come up from iTunes running in the background, or could Cydia (or maybe the theme) be a method of password phishing?
I've seen this problem come up, and the only jailbroken apps I have installed are NES, SHH, FlashLight, Intelliscreen, and MobileTerminal. I kind of think Intelliscreen 2.0 was at fault, since I don't remember it occurring before that, and haven't had that problem since I upgraded Intelliscreen to 2.0.1. (If you have Intelliscreen installed?)