tack:
Uploading small sketches is fine. I can load the blink sketch via serial every time. It only manifests with larger sketches, even 20k sort of size.
In my tests, the synch problems manifest both with small (Blink) o large sketches. Simply, without RC filter the chip doesnt' respond to the data sent through the serial line.
retrolefty:
It was a passing comment by one (or a couple of) avrfreaks poster that apparently sought out ATMEL's help, he was told effectively to clean up his circuit layout.
Uhm. this has a sense for me. Since today, I've only tested the 1284P on a breadboard because I didn't want to make a board for the serial programming using the bootloader if I wasn't SURE that I could do that to upload a sketch.