DVDdoug:
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.)
I bought 16 of these LED buttons: 16mm Illuminated Pushbutton - Blue Momentary : ID 1477 : $1.95 : Adafruit Industries, Unique & fun DIY electronics and kits
Try swapping the brightest & dimmest in the circuit. If the bright one remains bright on a different output, it's the LED.
Ok, I'll try this when I get home.
What is the resistor value? If the resistance is too low you might be "stressing" the chip and getting variations from that.
220 Ohms