The dependence on the initial pin configuration at power up of the esp8266 is expected
Next there is the OS you are using linux and windows.
XTCOM always messes up my Windows & pc requiring a reset since Windows won't shutdown after XTCOM messes up the comm port
EPStool has dependencies on a specific version of python
I use flasher.exe which works well under Win7 except for the leaving flash mode quirk which is worked around by unplugging from the port.
Flasher has issues; it flashes expressif electrodragon firmware bins but has issues with others.
This is the cutting edge with esp8266 so getting cut with bad documentation imperfect firmware etc is very probable.