I alo started a 1284p adventure, using this board.
Schematic and PCB of the board ATmega1284P: End to End using 1.0 IDE - #248 by system - Microcontrollers - Arduino Forum.
Uploaded the bootloader, following maniacbug blog without any problems.
Then I tried uploading a sketch with USB BUB-II (modern device).
But all I got was error.
I then placed the 1284P on a breadboard ( nick setup), and that worked.
On the diagram, you can find a RS232 interface, this makes a pullup for the RX line, the BUB couldn't pull down
this line far enough to work.
I cut the trace's to R9 and (R6/TXled), and now the board works fine for me.
Thanks to Nick, Manicbug , and all others contributing