I'm trying to create a matrix of 12 LED's, 4 of which will be dimmable with analog values, and they are using pins 5,6,10,11. The problem I'm having is that 5 and 6 are analogWrite to 0, yet the LED's are glowing at a very low level. I'd like to know if there is a trickle voltage or some sort of setting which is providing constant voltage from the 5 and 6 pins that I can't override with analogWrite.

I tried it and you're correct. I used pin 5 and it's fine digitally, the minute it gets a analogWrite it will never go completely off even if I set it to zero with analogWrite

BUT Try this:

In setup set the offending pins as outputs. analogWrite doesn't care

When ever you need a zero digtalWrite(pin, LOW);

I just tried this and it worked. I tried setting the internal pullup on and off with no effect so I'm not sure why those pins are acting up.