Buildcraft Wiki said:Note: clearing areas using the Flatten or Clear patterns
version - 3.3.x: Clearing is done bottom layer to top layer. Items dropped can be collected
version 3.4.x+: Clearing is done from top to bottom layer, items cannot be picked up in the first 1/2 second and vanish after a further half second. This change was made to stop the filler being used as a cheap quarry alternative. This can be disabled in the Buildcraft config file by setting the variable 'B:filler.destroy' to false.
Have you read the buildcraft filler wiki entry? You should check it out, about three quarters of the way down the page, below the pattern descriptions.
The config variable should have only changed the action taken when the filler spits out items, I don't believe there is any way to directly change the direction in which it clears from.