The difference is coming from the Vref used for both these measurements. If you are using 145 kit for this test, it uses 5 V VDDA, therefore Vref chosen for normal scanning is 2.74 V. But BIST uses Vref as 1.2 V (~2.25 times lower), that is why you are seeing this difference. If you make Vref as 1.2 V for normal operation (not required / not recommended), you should be seeing the same rawcounts.
Also from your project, button0 is a mutual capacitance button. Rawcounts of CSX button translates to Cm and not Cp. BIST performs CP measurement only. You should be probably looking at Button 1 or Button 2 where you have configured each tx or rx segment as CSD buttons. From your description, you should be looking at BUTTON 1. Please check this.
I ran your code with Vref set as 1.2 V for normal scan (using expression view - not recommended/ needed). I compared the rawcounts of BUTTON1 (RX segment connected as CSD button). The rawcounts obtained from the normal scan and BIST scan were same.
Thanks very much! If I want to set Vref as 1.2V, should I connect my VDDD to 3.3V?
Please note that you will achieve more signal for higher Vref. Therefore, we recommend selecting the highest Vref possible for the given VDDA (chosen by component).
Vref can be set to 1.2 V by following any one of these techniques (For experimenting only):
1. Using Expression View -
a) Go to Tools > Options > Design Entry > Component catalog and check the Enable Param Edit Views option.
b) Open CapSense component. Right click on Advanced tab. Click on Show Expression view.
c) Under CSD Settings, enter 1.2 in CsdVrefV2 field. Default is -1 that chooses Vref based on VDDA.
Note: Do not modify any other parameters in the expression view. It will lead to unexpected Capsense behavior.
2. Change VDDA < 2.6 V to choose Vref as 1.2 V. Also ensure that you have changed the values of VDDA and VDDD under systems tab as well. This will be used by the component to select Vref automatically.