We request you to use the CapSense Tuner GUI and check what is happening actually in case of Auto (smart sense) and manual tuning.
Ideally there should be minimum of 5:1 SNR (Signal to peak-peak noise ratio) in case of any CapSense sensor. If it is not you should adjust the CapSense hardware parameters and software thresholds in such a way that SNR of 5:1 is achieved.
You can use the PSoC Creator code example on Tuner to use it in your project. Please go through the CapSense Tuner Guide obtained from the link below. The spec shows obsolete but you can use it because it is designed for old CapSense component which is used in PSoC 5 devices. If you use PSoC 4 the CapSense component will be different.
Also for proper operation of Auto Smart sense the parasitic capacitance of the sensor should be in between 5pF and 45 pF. Please measure the sensor parasitic capacitance using the API GetSensorCp(). Please refer CapSense component datasheet for more information of this API. You should run the project in debug mode to measure the Cp. For manual tuning it can be upto 65 pF.
Please check the above points and update us. If possible please attach the complete PSoC Creator project along with Layout files in gerber format so that we can review them and provide you our comments.