This happens occasionally in our lab as well, both HPLC and GC, and believe also with our LAN-communicating ones. When this happens we do what our outsourced consumer information lines tells our customers when the scrub doesn't come out of the containers: "You must re-boot".
So turn of the instrument including autosampler module, turn off computer, turn on modules, start up computer. Then start up ChemStation. Sometimes we find that none of the clicks on the computer will work, and we can't even shut down Chemstation or Windows, must physically power off or unplug the computer and start again.