Just as the title indicates the filler will not clear for me. I can clear small areas but when I get near the edge of the max radius it stops working for no apparent reason. I've made a video showing the way I set it up which has always worked in the past for me.

https://www.youtube.com/watch?v=o7sERxwmlDQ

Maybe I'm missing something stupidly obvious if so I apologize.

The behavior is the same with energy conduits and pipes if that matters.

Update:
I decided to just try using smaller fillers because I want to get this done and that worked... until it didn't.
The filler pictured here:
http://img.techpowerup.org/140712/Capture595.jpg

was 5 blocks taller and the same in all other dimensions. It worked for a few layers then stopped for no reason. I tried placing it as pictured to see if it would work again but no dice.

Ah. I'm an idiot. Didn't know that they stop if they hit lava. GG.