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.
I worked for a while with Atmega1284P in the past weeks and I also experienced problems during the upload of a sketch using the bootloader.
I looked for help on the form (here and following posts) then I googled and found on AvrFreaks that this could be an hardware bug on the USART0 (read here).
So I solved using an RC filter with a 10K resistor in series and a 100 pF capacitor to ground, both put very close to the TX RX pin of the Arduino 1284P. Also, cut a little the pins of the capacitor.
Try it.