The caps on the crystal are .022nf and the rest are .1nf. The crystal is 16mhz and the resistor from reset to 5v is 1k.
Can anyone see what I am doing wrong here? I know the FTDI board works as I have used it to program other avrs, but I have never burnt a bootloader before. I know it did something as the fuse bits changed from the defaults, but I don't know of another way of testing to see if it was successful.
Uh, I just looked at the output from "burn bootloader". It looks like the board definition you had selected didn't use a bootloader - I just see it setting the fuses, not writing a bootloader.
The first log you've sent looks promising but it is just reading the fuses as DrAzzy wrote. Did you burn it? You can read the flash to check if bootloader is present.
I don't think that the problem is bootloader uploading. Your setup for ISP must be correct since it works. You can prove it by reading the bootloading part of the flashmem via ISP and data have to be same as BIN of bootloader. So the problem could be a bootloader or something else.
Did you used correct version? F_CPU must fit.
Early after reset at the start of bootloader L should to blink fast 3x.
Is your wiring for upload via bootloader correct (Rx, Tx, DTR/RESET)?
I'm pretty sure the wiring is correct, like you I don't think there is a problem with uploading the bootloader. I will look into verifying the data on it.
A few questions:
I'm using the optiboot_atmega1284p.hex by JChristensen. Which pin on the 1284p should I connect a LED up to to verify that it blinks on boot? Also I found some old bootloaders from maniacbug
ATmegaBOOT_1284P.hex
ATmegaBOOT_1284P_8MHz.hex
Should I give them a shot? In particular the 8mhz one, am I correct in assuming this will work without the external crystal? Just to eliminate one possible source of error (ebay crystals).
None of your posts show Avrdude being given the command to actually upload a bootloader. There should be something like -Uflash:w:NameOfBootloader.hex:i at the end of the Avrdude commandline, I don't see that. Does your boards.text file show a bootloader name and path? The output you have posted looks exactly like what you get when you invoke Avrdude without instructions to do anything. It initializes the micro, reads the fuses and then exits.
Mighty has L led on PD5. Follow the variant and D13 Arduino port in the file pins_arduino.h e.g variants/standard/pins_arduino.h. Also you can use 'non crystal version' to exclude problems with crystal. However there is simple way to check crystal oscillation with multimeter on XTAL1 pin opposite to GND. DC voltage should be cca half of VCC. 2.5V should be if VCC=5V, since there is 50% square signal.