My first guess would be that the wire connections on my ESP-12E somehow weaken the strength of the signal compared to nodeMCU's PCB connections. But this seems to be a really last resort reasoning and I'm hoping there is something in calibration of these chips that I am missing. Even though I am burning both the flashes with exactly the same software(down to init_data_default and blank.bin files). Is there something else that can impact the performance except code and layout of wires?
If it's helpful I am using an AMS117 3.3V converter on my ESP-12E setup; the same as used on a nodeMCU board.