Verification errors in custom mega

We are designed custom board using atmega2560. Initial bootloading and program upload is successfully done (using uno for bootloading and upload removing the main IC atmega328p) . The board works fine with boatloader USB port connected to PC and supply is given to atmega2560 using bootloader 5V and ground.
Problem arises when I power the board with external power supply (230V AC to 5V DC ).

There is weird issue that the program works properly only when the uart pins are still connected with bootloader uno board .

Custom PCB RX --> RX ( UNO boatloader)
Custom PCB TX ---> TX ( UNO boatloader)

In this case is not supplied with any power in bootloader uno just connected.
Initially I connected tx and rx with bootloader uno its work and after I remove Rx & Tx pins its work fine.

Could anyone let me know where exactly I am doing wrong
Thank you

Load a minimal sketch to the the Mega (one which say prints "hello world" to the console) and see if the problem remains. If so, post the code here.

in this case we can't see any serial monitor because its work with external power supply. i tried blink also its won't work and again i connected with non power uno(removed atmega328p) Tx&RX pins it will work. In this case here Intially hardware wants something to pull the data. please help me guys

And post a schematic of your custom atmega2560 board.

Did you test the layout and connections on a breadboard before designing the PCB ?

Is the power supply 0V tied to the serial (programming) ground as well ?

It sounds like some sort of phantom powering is involved or the board has other dependencies on the connected Uno, for example the reset connection. Maybe measure the resistance between the Mega reset pin and Vcc when the Uno is completely disconnected. 10k is normal.

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