When Nautilus is in browser mode, and a new window is opened (either with ctrl+n or from the "File" menu), the new window always opens with the home directory. If you are several directories in and merely wanted to compare the contents of two directories near each other in the file system, you have to switch back to the old window, click the "Toggle between button and text-based location bar" button and copy + paste the text into the address bar of the new window.

It would make more sense for the new window to open showing the same directory as the old window, since it's easier to click the "Home" button than it is to navigate back to the same place as the old one.

Other information: