I am not familiar with FC3, but the most likely things that would cause such an error, IMO, are
- You already have an apt process running (possibly one that failed while running). Check your running processes (top etc.), or reboot.
- Unwittingly, you installed a broken copy of Apt. Try removing and then reinstalling.
- You are attempting to run Apt from a 'live' copy of FC.
Presumably you've already looked in /var/lib/apt/lists, and it's empty ?
Cheers,
mj