I really really like your plugin and even purchased the ids and predefined styles which are both great!!!
There is are 2 problems with RTL wesites with the Layers of the Ultimate TinyMCE plugin.
1. the entered div is either absolute or nothing. absolute is not a good configuration for this as on the website it appears out of the post... the attribute should be relative.
2. on RTL websites there is another problem, the positioning of the div is from the left which is problematic as the Reference point is from top right. when the website is LTR the Reference point is from top left.
Another thing, is it possible to make some visual areas round inserted SPAN. Once I insert a SPAN I can't find it in the editor. It makes it very hard for my customers to use the SPAN button...