I know this problem has been reported multiple times but in my case I think there is a different light on it.
My desktop is a w7x64 box and I also have a notebook with w10.
Both system have the arduino IDE 1.8.5 with the latest updates.
The desktop though has more boards and drivers as it is my main development system.
I have at ATmega2560 clone with CH340 which used to work on my desktop about half a year ago when I tried to get an LCD touch shield to work.
Yesterday I tried to resume on it and I got the ubiquitous timeout error.
So I removed the shield and tried the basic blink sketch but no change.
I tried an arduino nano and there was no problem to upload the blink sketch.
Then I tried different USB cables and ports but the timeout problem with the ATmega persisted.
So I went to the notebook and the ATmega worked like a charm.
Now I know that the board is ok as well as the cable.
The port is also ok as the nano worked on it smoothly.
I also tried the upload from an elevated command prompt with the verbose option but it gave me no further clue.
The output is below:
C:\Users\Pete\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino14/bin/avrdude -vvvv -CC:\Users\Pete\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0-arduino14/etc/avrdude.conf -v -patmega2560 -cstk500v2 -PCOM34 -b57600 -D -Uflash:w:T:\TMP\arduino_build_330193/Blink.ino.hex:i avrdude: Version 6.3-20171130 Copyright (c) 2000-2005 Brian Dean, http://www.bdmicro.com/ Copyright (c) 2007-2014 Joerg Wunsch System wide configuration file is "C:\Users\Pete\AppData\Local\Arduino15\packages\arduino\tools\avrdude\6.3.0 -arduino14/etc/avrdude.conf" Using Port : COM34 Using Programmer : stk500v2 Overriding Baud Rate : 57600 STK500V2: stk500v2_open() STK500V2: stk500v2_getsync() STK500V2: stk500v2_send(0x1b 0x01 0x00 0x01 0x0e 0x01 0x14 , 7) avrdude: Send: . [1b] .  .  .  . [0e] .  .  STK500V2: stk500v2_recv(): avrdude: ser_recv(): programmer is not responding avrdude: stk500v2_ReceiveMessage(): timeout
Does anybody have an idea how to further tackle the problem?