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From your description, this is not a software issue. It's a hardware issue.
I suspect the PSoC target is not coming out of RESET state on its own. When connecting Mimiprog, Miniprog toggles XRES thus resetting target. And/Or, Miniprog is providing power to target just enough to get it running and you have a powering design issue.
To test the RESET issue: - power up your pcb - momentarily touch a wire from XRES to Ground If PSoC starts working this is the issue. If PSoC doesn't start working, next momentarily touch a wire from XRES Vddd. PSoC has now been reset.
As another test, you could connect a pull-up resistor (anything from 4.7k to 20k) from XRES to Vddd and see if pcb will come out of RESET state.
If the power supply is the issue, we'd need to see your schematic (pdf or screenshot would be fine).
Thank you for providing schematic image. I see an issue with schematic power connections.
Vccd - there are 2 Vccd pins to connect together. I think your schematic has done this. However, Vccd should not be connected to Vcca. Vccd and Vcca are regulator outputs that need independent capacitors. Disconnect Vcca from Vccd and add another 1.0uF capacitor. After doing this modification, re-test the pcb.
I see you have location for XRES pull-up resistor and capacitor. This is good. You can increase the capacitor to 1uF as this will give more RESET state as power supply rises in voltage. I will say, 1uF might be too much for Miniprog to discharge quickly. So, you might need to experiment with a capacitor value in between 0.1uF-to-1uF (to have Miniprog work correctly).
Something else to try is, remove XRES pull-up resistor. Re-test pcb. And then, remove XRES capacitor, and re-test. This would be similar setup as KIT-059 with PSoC 5LP.