Show stopper indeed.. I haven't heard of it happening thusfar (maybe IVO has), and windows 7 compatibility should be pretty high, as it hasn't changed much. (unlike windows 10) but consider trying an older version of classic shell just in-case one of the new features broke compatibility.
https://sourceforge.net/projects/classi ... 20release/ being the most likely to work correctly, assuming you dont need the windows 7 style, or a customized taskbar.
You mention that they keyboard still works for 'win+r' does that mean that the keyboard functions normally for everything outside of classic shell when the error occurs? If-so you can right click and select exit to close classic shell, and then run it again from the default start menu.
I havnt used macro express, but I have used keytweak with classic shell and without incident. *IIRC all it does is write the changes to the registry anyways*