I only have the second generation car.
When I read it initially, I thought you have pressed the button that deactivates the use of the windows. Does your car has that? Did you try to play with it and notice what is going on? If nothing like that is going on, I would carry on to the next bit, the fuse.
That about the fuse and the box, is a bit extreme. I would check the manual, locate the fuse, take it out, inspect it and if it seems OK, I would replace it just in case that is the problem. If the new fuse does not do the trick, then I would ask an auto electrician to check it. Replacing the fuse box should be a big job which means that you have a great potential to create big problems. I know the garages want to play around swapping stuff, but this does not usually fix the problem if they do not know that this is the problem. If the cost to fix the windows is reasonable, go for it, otherwise if they ask you a fortune to make them work, stick with the drivers only for time being and keep investigating.