In Yosemite, I could use CMD + ~ to switch between windows of an application, but it switched only between windows on the same desktop/space. When I use the same keyboard shortcut in El Capitan, it switches to windows of the same application that are opened in other desktops. Is there a way to restrict its behavior to within the same desktop (the way it worked in Yosemite)? Thanks!
As linkedlist suggested, I updated to 10.11.1, which fixed the issue when using Chrome. However, I find that PHPStorm's windows still behave as described above.