I've built what I believe to be a Arduino compatable board based on these boards: http://arduino.cc/en/Main/ArduinoBoardSerialSingleSided3
Mine uses the FT232R like the Diecimila and uses the cap coupled DTR for AVR reset.
Board works using CodeVision AVR and Bascom and I use an older Atmel AVR ISP (RS232 version). I'm having limited success with the Arduino IDE, I'm using Version 0022.
Scenario #1 Using a M168 P and set the board as a Diecimilia with a M168 I have no sketch downloading success regardless of bootloader loaded via the AVR ISP and AVR Studio. Always ends with a AVRdude error no sync....
Scenario #2 Using a M328 P and using the ADAboot loader and setting it to either a Pro 16mhz M328 or the Duemilanove M328 I can download a sketch once and it executes fine. From that point on though the only way I can get it to download a sketch is to reload the bootloader with the AVR ISP via AVRstudio. Using a hardware reset, the sketch starts running again or power cycling the same.
My guess is the sketch is overloading a part of the bootloader or something or the reset startup fuse setting is an issue.