KB001695: What are the Steps to Troubleshoot why AutoIntegration is not Integrating Peaks as Expected? - MS ChemStation 

AutoIntegration uses software to generate the analysis conditions based on the nature of the peak, variations in the base line, and similar factors. These values are entered into the analysis conditions (the conditions set in the [Analysis Conditions Settings] screen) and used for integration. As these are determined by software, they may not match what a person would choose. If integration does not work correctly, refer to the explanation of how to set the integration conditions in the [What to Do If Quantitative Values Cannot be Obtained] section in the Appendix.