Handles: I've not yet addressed any other handle positions except the se for resizing. Its on my todo.
Scale: I was unable to reproduce your problem. I am using "transform: matrix(a,b,c,d,e,f)" instead of scale, rotate and skew. Try using the functions built into jquery.transformable.js to apply your transformations and it will translate them into the proper matrix values. Example:
$('#mybox').setTransform('scalex',2);
$('#mybox').setTransform('scaley',2);
That will set the scale in a cross-platform way and allow it to interact with the rest of the functions in jquery.tranformable.js.
If that doesn't work for you, please set up something on jsfiddle for me to look at and I'll see what I can do.
Also, I may have stopped calculatiing the total transform of a nested object before <body>. I'll look into that. If that is the case, in the mean time you might be able to just wrap everything in your body in another 100% sized div and apply the transform to that.
Cya,
-A-