Tested filler and by making a 24x24x1 area and set it to flatten and it began adding blocks really high above the area i selected

Same as #1644. The general rule is to start open issues on http://mod-buildcraft.com/forums/index.php?board=2.0 so that all users can work, and to upgrade these on the tracker when issues are confirmed and ready to be worked on. As for the other one, as a matter of fact, fixes are already included in the future 6.0.7.

Thanks for your help!