I had a weird experience when I first got my iBook, which is probably not related to this. When I first got it, I had no USB devices, except for my printer, which was living on the AEBS I bought with the computer. So I didn't actually even try the USB ports right away. A friend bought his digital camera over and I wanted to look at pictures he took. It would only work in one of the two USB ports. We unplugged it and plugged it and tried it several times, and this was consistent. Some other devices exhibited the same behavior. A short while later, when I got my first digital camera, I tried this again, and oddly, it was working fine. And has never been a problem since. But I can't explain why it didn't work when I first got the computer.
Anyway, I think you should march up to Apple. Even if you have an issue like mine, the onus should be on them to fix it. You shouldn't have to figure out something crazy like that.
