CrossRoads:
The only times I have trouble with serial downloading is when I accidentally leave the DTR cap off, or forget to burn the bootloader first. I'm slowly getting better about that!
So OK fess up. Did you purposely do some 'special' PCB layout for the clock/RX0 lines on your 1284P boards being aware of the possible problems of noise interactions with serial communications? Or did you just get lucky. 
Lefty