I developed a custom board with the ATMEGA2560 controller and I try to program it with the Arduino IDE (V1.0.1) through an Arduino Uno board (using the serial and reset signals + GND).
The custom board has the ICSP connector and with the AVRISP MKII I am able to download the bootloader and any other sketch.
The problem is that after downloading the booloader (with the AVRISP MKII) I am able to download only once any other sketch with the Arduino UNO configuration. (In the Arduino IDE I set Board=Arduino Mega 2560 and Programmer=AVR ISP).
I'd like to know is someone else tried to do the same and which kind of working solution he found.