To reproduce:
1) Open Tools|Options|Environment|Keyboard, type "rename" in filter and set "Ctrl+Shift+G" (or any other but unique) shortcut to the RenameFile action
2) Open some project
3) Check if the shortcut is working, select any cpp file in project explorer and press "Ctrl+Shift+G" - does not work
4) Open context menu over the same cpp file and press "Rename" action - this works
5) Now select the "Sources" node without opening the context menu, press "Ctrl+Shift+G" - you can start renaming sources node which is not desired

Basically the same happens for all other actions in project explorer since actions are enabled/disabled only when we are going to show the context menu. I think it should be updated whenever the current item changes.

If these actions are not designed to possess shortcuts this should be somehow blocked in options.