Ahh..
Had the same problem. I am using a Mega1280 as the host Arduino for the WiFi shield.
I have a Webclient sketch that would connect only when the USB (useb to download and for the serial monitor) was connected. Added an external 12v power supply and found it would not connect ( no green LED, nothing sent to the server) I found that pressing the reset a few times ( on the base Arduino or the Shield) would start it up....h'mm ....I had pins 7 and three jumper-ed as suggested somewhere. So I whet back to the drawing board and re-read : http://arduino.cc/en/Guide/ArduinoWiFiShield#toc2..there was the answer..
in the section on using the Shield with older boards...
"put a jumper in from the 3.3 V pin to the IOREF pin on the WiFi Shield..."
As there was no reference to adding a jumper from pin 3 to pin 7; I removed it. I don't remember were I found that instruction
Did that and and it now connects and functions with no USB connected and just an external power supply.
David G.
Gaithersburg MD