Communication with computer

My GC uses Chemstation Rev A.08.03. The computer that came with it is an old model system. It crashed and I had to get a modern system. I have installed the software on to the system and the computer can see the GC. However, there is a very big time lag between the system and the GC. When I am running a sample, the solvent front peak doesn't come out not until about 5 to 6 minutes. This is affecting my results. What could be wrong please?