hi sorenmt84, sorry to see that no one responded.
You're right, the Eye-Fi card can still upload to online destinations like FTP servers even if the computer is turned off.
If you're still experiencing this issue, please try the following steps.
First, quit the Eye-Fi software: look for the Eye-Fi Helper icon on your computer screen (in the Windows task bar or Mac/Apple menu bar), click it, choose Exit/Quit and then Yes to confirm. Shoot a few new photos onto the Eye-Fi card, with the card/camera very close to the router (5-15 feet if possible). Wait a few minutes and see if they upload to your FTP server. Check the Eye-Fi web site http://center.eye.fi
to see if any have arrived.
If not, please remove the card from the camera, relaunch Eye-Fi Helper, and send us your Eye-Fi card log using the instructions in this post: viewtopic.php?f=30&t=5776
You can post the log here or email it to email@example.com
with a link to this thread.