tack:
I get the same issue with teh 1284P using Mighty1284 Optiboot (Bobuino pinmap).I can upload Blink but not larger sketches. I eventually gave up and just program via ISP. It's a bit of a pain for serial monitor as I have to keep switching my USB>TTL adapter to monitor, but I'm just going to order another cheap one to use with MTTTY for monitoring.
I have seen mention that trying a swap of the crystal resonator, or switching to a ceramic resonator can cure it, but I've not tried that as yet.
If anyone does know a link to a definitive fix then it would be useful to knoe.
This really sounds like the 1284P DIP internal hardware bug effecting the serial input pin. The folks over at avrfreaks site had lots on it in the past. Seems the fix is to wire a low pass filter to the serial input pin which is a .1 ufd cap from the rec pin to ground and a series 10K resistor from the pin to whatever is supplying the serial data. Date code on the chip may or may not help identify a vulnerable chip. Another fix is to use a bootloader for the 1284P that was been compiled to use the second serial port on the 1284P that wasn't effected by with internal hardware bug. There was such a bootloader made available a while back by someone. Who remembers all those details. 
And of course these days you can use a arduino board running the arduinoISP sketch and upload your sketch using the IDE file/upload with programmer option the IDE now offers.
Lefty