I'm using an Arduino plugged into (via a USB cable) and thus powered by a BeagleBoard running Ubuntu Linux. It boots up fine.
I suspect it's a problem with your BIOS. When a computer boots up, sometimes it tries first to boot from a USB port, thinking that there is a pendrive or hard disk there to boot from. When it finds something on the USB port,even though that something is not a boot device, it hangs.
I've had that happen to me in Windows with a USB wireless mouse dongle. I've not had it happen in Linux. But I suspect that may be your problem.