Scale tool problem
 

Alright so my scale tool is acting kinda funky, right now the Y and X Axis are flipped and when I freeze transformations it just tilts the scale tool, posting screens.

and this is what happens after i do freeze transformations, before hand everything is straight just flipped:confused:

Check your Hypergraph and make sure the item isn't parented to something else. If it is, that could make it not line up after using freeze transformations.