I have also a esp8266 boards package 1.6.4 in a backup ~/.arduino15 folder (modified to work with my NodeMCUv2, ->dio flash layout). If I use the old folder (v1.6.4) and build and flash the image(s) with that package the board boots without problems and executes the built program - with the same GPIO0/RST wiring I used before.
My NodeMCUv2 can be successfully flashed with both, esp8266 1.6.4 and 1.6.5 and both versions boot.
I tried overriding the flash layout by adding a "-bm dio" parameter to esptool, no change. Also I tried using esptool 0.4.4, also no change. I conclude therefore it seems to be related with the binary flash image.
Does anybody have an idea?
Thanks