When using the advanced linking tool, all the drop down menus are not returning any values.
Using chrome the console shows the following error when the modal is triggered:
Uncaught TypeError: Object [object Object] has no method '_add'
I know it's very early in 3.5, but I thought you should be aware of the issue given how many people use your plugin.
I've tested this running 3.5 with Twenty Twelve, and no other plugins activated except the TinyMCE Advanced