It sounds to me like the player is getting too far into the "wall" tile before the hit test occurs.
My guess is that the call to FlxObject.separateX() is finding 0 overlap and so it skips that and goes on to separateY(). You could maybe confirm that with some trace() lines.
How big is your player asset compared to the tile size? Maybe try making the hit box slightly bigger or smaller by a few pixels so that it doesn't match a tile exactly during a hit test.
Edit: You could also try moving the player more slowly (in increments less than your tile-size), just to see if the framework picks up the collision better that way.