Reading the SAM3X main datasheet it says the following in section 32.5.1;
Pull-up Resistor Control
Each I/O line is designed with an embedded pull-up resistor. The pull-up resistor can be enabled
or disabled by writing respectively PIO_PUER (Pull-up Enable Register) and PIO_PUDR (Pull-up Disable Resistor).
Writing in these registers results in setting or clearing the corresponding bit in PIO_PUSR (Pull-up Status Register).
Reading a 1 in PIO_PUSR means the pull-up is disabled and reading a 0 means the pull-up is enabled.
Control of the pull-up resistor is possible regardless of the configuration of the I/O line.
After reset, all of the pull-ups are enabled, i.e. PIO_PUSR resets at the value 0x0.
Notice that it mentions all pull-ups are enabled after reset.
I wonder if maybe something has been overlooked in disabling pull-ups on setting pinMode(x, OUTPUT)?
On 2 separate Dues, I set an LED + 100k resistor to pin 25, which lit up on initialize
I am surprised you were able to see any light emitting from the LED at all with a 100kΩ current limiting resistor, you must have exceptionally good eyesight ?