you do have the board powered during programming, right?
no cold joints on the db-9 connector?
i've built a bunch of these as minipovs, minipovs with uv leds, brain machines, rgb brain machines, 4x4x4 led cubes. all programmed with linux. either opensuse or whatever it is that's on my eeepc.
with the led cubes i had to disconnect the leds from the programming lines to program the chip, but never had a problem with single leds on those lines.
"i want to lead a dissipate existence, play scratchy records and enjoy my decline" - iggy pop, i need more