I decided to take up burning the bootloaders with atmel studio as the only way i ever got it to work from the arduino IDe was with the arduino uno programmed as the ISP which is hideously slow and sometimes i need to do a few.
So i looked up the boards file and identified the fuse settings: 0x05, 0xDE, 0xFF, extended - low, if i use these and read them back after programming the extended fuse is not 0x05 but 0xDF, why is this ? setting the stated fuses in the boards file (and all over tutorials online) does infact flag some yellow exclamations in the programming window which go green after programming and the revised fuse setting has gone in which i seem to have no control over. As far as I'm aware the chips work fine.
I'm assuming that doing the main hex file first or doing the fuses first makes no odds ?
what about the lock bits ? these are rarely mentioned in tutorials but some do.
Alternatively is there a way of speeding up the arduino programmed and an ISP ? but i guess not because the board pretends to be a serial connection to the PC which is max 115 Kbps.