What affects LED brightness?

It's not the soldering...

The first thing I'd suspect would be the LEDs. Are the LEDs all the same part number? Did you buy cheap LEDs? (Good LEDs can vary too... Usually the datasheet shows a minimum brightness and a typical brightness, at a specified current, but no maximum.)

Try swapping the brightest & dimmest in the circuit. If the bright one remains bright on a different output, it's the LED.

Resistors have a tolerance, but I'd be surprised if 10% resistors (the "worst" commonly available) would make a noticeable difference.

What is the resistor value? If the resistance is too low you might be "stressing" the chip and getting variations from that.