The problem with nested comment is originated that the “comment form popped below the comment you want to reply” effect.
The WordPress built in function (maybe from theme I suppose) “copies” the original one and place it below a specific comment, and hides the original one. However, it does not move TinyMCE keybinds, i.e. “Click this specific place will bold the text I highlight”, “type any keys into the custom built JavaScript Object”, blah blah blah… And so it seems “locked”, does not react to user keystrokes and mouse clicks.
I don’t know if that could be solve by the modifying the plugin or the theme or WP itself, and currently I don’t have the time to look into…