You do have current limit resistor in the LED path, yes? 220-270 ohm or so?
Regulator is knocking 9V down to 5V all the time.
Power LED is on.
Board draws ~15mA when running a simple loop for regulator, atmega328, USB/Serial adapter, power on LED.
9V batteries only have something like 300mAH of capacity.
300/15 = 20 hrs tops.
I'd suggest a 7.5V wallwart for power.
Example: Switching DC Wall Power Adapter 7.5V / 1A - dipmicro electronics