Cycle application windows changed in recent update (2019)
I use PhpStorm 2019.2 on macOS 10.14.6 Mojave. The behavior/logic for CMD + ` is not any different from how it has been in any relatively recent version of macOS or PhpStorm.

Pressing CMD + ` switches to the most recently used window, unless you haven't done anything in the currently active window, in which case it switches to the next most recently opened window (and this pattern continues for however many windows you have open).

For example, let's say you have a file open in PhpStorm in window A, then open another file in window B, and finally a third file in window C. If you're working in window C and then press CMD + `, you'll be switched to window B. If you press CMD + ` again before doing anything else, you'll be switched to window A. However, if, instead, you work on the file in window B first, then when you press CMD + `, you'll be switched back to window C (the most recently open window). In order to reach window A, you must press CMD + ` twice without doing anything in the window that comes up after the first window switch.