OK I think I have confirmed it really is in the bootloader. I'll take a look at the bootloader code when I get a chance to see if I can find where pin 6 is getting set.
mrmeval:
The pullup resistor is supposed to be 20k - this is controllable by software - inside the chip. When you hook up an LED you are are reading the forward voltage of the LED. Even though the pin in configured as an INPUT, the pullup resistor is plenty to power an LED with a faint glow. Or show up on a voltmeter.
This is a little confusing:
When you do this:
pinMode(6, INPUT);
digitalWrite(6, HIGH);
It's not making the pin an OUTPUT - still an input but turning on pullup resistors
pinMode(6, INPUT);
digitalWrite(6, LOW);
turns off the resistors but still keeps the pin as input - the pin is then high impedance input ~ 100 M ohms
pinMode(6, OUPUT);
makes it an output - I think it defaults LOW
to make it HIGH just do
digitalWrite(6, HIGH);