It's pretty clear that the problem symptom is real for many people, as well as it's true many people have not seen the same problem symptom. The low pass filter does seem to be a 'solution' for many that are seeing that problem. Atmel does not seen to have ever claimed it's a chip internal problem, but rather they speculate that it's most likely a problem that may be caused by noise coupling from the chips clock lines pin(S) to the RX0 pin, so circuit layout external to the chip may be a variable that increases or decreases the possibility of one having the problem, and is supported by the observation that it's only been seen in DIP packaged 1284P chips. Changing to a bootloader that uses the second serial port has been a solution for some that have experienced the problem also.
My participation on this topic has been mostly academic and I just mostly passed on what I had read on the avrfreaks site (which I consider credible on this topic), and from what I've read on postings on this site. I'm still waiting for my 1284P chip to arrive from a slow boat from China (Futurlec, known for good prices and slow deliveries). So far using CrossRoads' 1284P through hole duem.. style board, I've seen no uploading problems using a 644P chip (even with a 60KB test sketch), but I am at least now knowledgeable to know what may or may not happen when I finally do get my 1284P, and possible solutions if indeed I see the uploading problem.
Lefty