Hmm I can't reproduce this in flashplayer 19 or 20, scaling is working for me on the dev branch of flixel.
As a quick suggestion, try doing
and
Sometimes when working with stuff like scale a sprite can get offcentered and move around in ways you don't expect... although in the code you posted above it should be fine.
Also try seeing if the sprite's hitbox shows up? (~ to open console and hit the top right button in the console, or do FlxG.debugger.drawDebug = true somewhere in your code)