When you load ESP8266Flasher.exe, the default configuration in the "Config" tab has 4 entries
x INTERNAL://FLASH At 0x00000
x INTERNAL://IROM At 0x10000
x INTERNAL://DEFAULT At 0x7C000
x INTERNAL://BLANK At 0x7E000
All 4 entries are selected. If you want to upload a new firmware, only select 0x00000, give the correct file path, unselect other 3 configuration and flash.
I had kept all 4 entries checked.
This worked for me. It may or may not work for you but just something to try at your own risk