My mega only works on 1.0.1 IDE My mega usb/serial adapter died some time ago, so I bought an external FTDI programer wich I got working on 1.0.1 IDE. I can load any program to the mega, even complex led matrix driver I wrote myself so the ATmega works fine and the external FTDI board does too. Strangely enough I if I want to update the IDE (tried once on 1.0.5 and yesterday downloaded 1.6.5) I get an

 avrdude: stk500v2_getsync(): timeout communicating with programmer


When this problem occurs, I see that the programmer board recieves something (it has Rx and Tx LED's) the Mega resets but never sends any data back, which does happen on 1.0.1 IDE.
This happens on my pc, and on a laptop son no pc related problems.
I'd keep using this version but now I got an OLED display I want to drive (SSD1306 from waveshare) but I can't compile u8glib on 1.0.1 but I can on 1.6.5, however I can't get a simple blink example to upload with this IDE.

I suspect the DTR pin (reset pin) is handled differently and that makes the mega stay resetting until it times out.
What can be the problem here? How can I get more info from the console to solve this?
You need to add a 100nF (0.1µF) capacitor between DTR and RESET so it generates a pulse instead of a constant LOW all the time the port is open.

The older IDE uses an older version of avrdude. The newer version of avrdude with the newer IDE has extra code for manually manipulating DTR to get around some issues with new versions of the FTDI drivers.