Is that after the latest update? I changed the UI to follow the resolution.
It seems to remember changes per-map now, all though only did a few minor changes and looked.
As for the other problem though you can see in pic's, also select nodes and other sub menu's now located in this potion then under main menu.
1- selected Timed Traffic lights
2- Road selected, and next button there and selecting.
3- no sub-menu any longer, and have lights in roadway, can not do anything with these in any combination of keys and/or mouse clicks.
4- tried any of the above 3 options, manual, signs or switch lights all get "Node is part of timed script" only way to change this is to delete road or file in the directory.
5- I can a just lanes though add/remove crosswalks and such other buttons.