Are you using same firmware for both the projects? Please attach the project/s that you are using with PSoC as well as BLE module.
Please ensure that you are using latest version of PSoC Creator i.e. PSoC Creator 4.2 and the latest version of CapSense component (i.e CapSense_P4_V3.10 or above). If not, please install them immediately and check with latest firmware.
Please refer the schematic checklist in "Getting started with CapSense" application note. If you are not able to find the issue with the schematic please attach the pdf of the schematic of your custom board so that we can analyze the Schematic.
Please try to program your custom board with PRoC CapSense code examples in PSoC Creator and check whether you are seeing any issues.
Debug the application using the debug mode and pause the application after certain time. Please attach the screenshot showing where the execution is getting stuck inside the CapSense_Start().