I have had to reflash about of the original firmware over to the Falcon firmware this year, but I ALWAYS select the option in the pickit to supply power, I turn it on. write, do a verify, check the checksum is the same, then turn off the power option, then dis-connect. Move on to the next one.
I hope Dave get's some breathing room in the next month or two to update the programmer itself to show the color order. I think the self test can always tell you what it is in a few seconds so you could quickly choose the proper one to reflash.
What;s the difference between 0.0.6 and 0.0.4 that i have been using?