Does your hard disk have a two headed cable? If it does they must both be connected to the MBA so the disk can get the power it needs. If not you will need an external USB hub that has its own power supply. The MBA USB ports have a fixed amount of power available. If that max is exceeded the port is turned off to prevent damage.
I have the same problem on my Air. The message first came up while my iPhone was connected to it for some time. Since then, it pops up ALL THE TIME, whithout anything being connected to the USB port, at what appear to be random intervals that vary between about one hour and a few seconds. I have tried resetting the SMC and the PRAM, but no results. A quick search revealed that thousands of users are facing this problem, but Apple has yet to provide a solution. Please help!