struggling with similar issue.... nodemcu 1.0 (esp8266EX) - connected on com6, but back of board says connect at 9600.
serial monitor at 9600 can display correct messages at boot.. no AT command response, but then when i upload some simple code i get the following:

....
Features: WiFi
Crystal is 26MHz
MAC: ec:fa:bc:27:cc:12
Uploading stub...
Running stub...
Stub running...
Configuring flash size...
Traceback (most recent call last):
File "C:\Users\jph1l\AppData\Local\Arduino15\packages\esp8266\hardware\esp8266\3.0.1/tools/upload.py", line 66, in <module>
esptool.main(cmdline)
File "C:/Users/jph1l/AppData/Local/Arduino15/packages/esp8266/hardware/esp8266/3.0.1/tools/esptool\esptool.py", line 3599, in main
detect_flash_size(esp, args)
File "C:/Users/jph1l/AppData/Local/Arduino15/packages/esp8266/hardware/esp8266/3.0.1/tools/esptool\esptool.py", line 2848, in detect_flash_size
flash_id = esp.flash_id()
File "C:/Users/jph1l/AppData/Local/Arduino15/packages/esp8266/hardware/esp8266/3.0.1/tools/esptool\esptool.py", line 688, in flash_id
return self.run_spiflash_command(SPIFLASH_RDID, b"", 24)
File "C:/Users/jph1l/AppData/Local/Arduino15/packages/esp8266/hardware/esp8266/3.0.1/tools/esptool\esptool.py", line 948, in run_spiflash_command
old_spi_usr = self.read_reg(SPI_USR_REG)
File "C:/Users/jph1l/AppData/Local/Arduino15/packages/esp8266/hardware/esp8266/3.0.1/tools/esptool\esptool.py", line 562, in read_reg
val, data = self.command(self.ESP_READ_REG, struct.pack('<I', addr))
File "C:/Users/jph1l/AppData/Local/Arduino15/packages/esp8266/hardware/esp8266/3.0.1/tools/esptool\esptool.py", line 386, in command
p = self.read()
File "C:/Users/jph1l/AppData/Local/Arduino15/packages/esp8266/hardware/esp8266/3.0.1/tools/esptool\esptool.py", line 331, in read
return next(self._slip_reader)
File "C:/Users/jph1l/AppData/Local/Arduino15/packages/esp8266/hardware/esp8266/3.0.1/tools/esptool\esptool.py", line 2636, in slip_reader
raise FatalError("Timed out waiting for packet %s" % waiting_for)
esptool.FatalError: Timed out waiting for packet header
esptool.FatalError: Timed out waiting for packet header

any ideas - change usb cable, ports, confirmed the com not used elsewhere... any ideas?
FYI - the blue LED on the NodeMCU does flash once you start the upload.. flash a couple of times then stops.

Pressing the FLASH and holding down before the upload command or once it tries to connect etc there is no difference.