When reading from PRA ($f001\$f00f) the data direction register should be considered for all bits.

[Yazwh0]

It only looks like it's considered for the I2C bits, not the joystick data.

In via.c:

case 1: // PA
case 15:
	i2c_step();
	if (!debug) via_clear_pra_irqs(&via[0]);
	if (via[0].registers[11] & 1) {
		// CA1 is currently not connected to anything (?)
		return 0;
	} else {
		return (~via[0].registers[3] & i2c_port.data_out) |					//I2C Data: PA0=1 if DDR bit is 0 (input) and data_out is 1; usage of data_out and data_in is a bit confusing...
			(via[0].registers[3] & i2c_port.data_in) |						//I2C Data: PA0=1 if DDR bit is 1 (output) and data_in is 1
			(~via[0].registers[3] & I2C_CLK_MASK ) |						//I2C Clock: PA1=1 if DDR bit is 0 (input), simulating an input pull-up
			(via[0].registers[3] & i2c_port.clk_in) |						//I2C Clock: PA1=1 if DDR bit is 1 (output) and clk_in is 1, simulating a pin driven by the VIA 
			Joystick_data;
	}