I have just finished making my first Generation 7 1.4.1 board with an AVR 1284P at 20MHz and I came across a problem with the bootloader in the Arduino IDE Support v2.1.
I burnt the booloader easily using an Arduino Uno as an ISP, but could not flash any firmware afterwards with an Arduino USB Serial Light adapter from the Arduino IDE. AVRdue reported a timeout error, as if the bootloader wasn't present.
However, I found no problem when using the bootloader from the earlier version the Arduino IDE Support - version 2.0.
I Hope this is useful information.