Full chromatograph is shown in the online version of Chemstation, but only the first half of the trace is shown in the offline version. Any suggestions?

What revision of ChemStation are you running? 

In Offline Data Analysis if you go to Graphics>Signal Options do you have a custom range specified?

I am using Rev.B.04.03-SPI{87}, and I have the range set to full. Just tried to change it to 0-16 which should show the whole scan, but the same issue occurs.

In that case then this could indicate that the conf_off.reg file for the instrument is corrupt. Try deleting the conf_off.reg file located at C:\Chem32\#\ where # is the instrument number. Then launch an offline session and see if the problem is still there.