MarkT: You should program at 5V supply rather than 3.3V if you can. If I'm flashing a bootloader I do it twice in a row to burn it in more solidly (I don't know if it makes any difference, but it shouldn't hurt).
We're being superstitious here. Nothing wrong with a 3.3V supply for programming. I have long ago stopped using 5V and all my arduinos run at 3.3V with zero problems, one at 24Mhz, although I do so at my own risk.
Also the bootloader is checked during programming, re-burning wont do anything but erode the internal flash cells. Thats similar to suggesting to delete contents on a flash drive and copy them twice just to make sure they get there. If a mismatch is found the software will return an error, unless verification is disabled, which is not default.