Drop-down menus appearing in the wrong place

I recently upgraded from Yosemite to El Capitan 10.11.6 on my 2013 Mac Pro. I'm having issues with drop-down menus appearing in the wrong place. In particular, when I open up an application, whether it's a Finder window, iTunes, Chrome, Firefox, PowerPoint, or something else, and open a pull-down menu, the menu will appear in the right location. If I then close that drop-down menu, move the application window, and then open any drop-down menu, the position of that drop-down menu will be shifted. El Capitan appears to be using the size and position of the application window when it opened to determine where the drop-down menu is positioned. Drop-down menus at the top of the screen do not have this issue, as their position is fixed.

As an aside, I upgraded my 2013 MacBook Pro from Yosemite to El Capitan 10.11.6 the same day that I upgraded my Mac Pro. I have not experienced this issue on there. Both computers are running the same applications. I use HyperDock and Macs Fan Control on both. Disabling HyperDock has no impact on this issue.

Has anyone encountered a similar issue before? If so, were you able to fix it? If not, my only hope is that upgrading to Sierra in a few weeks will fix the issue.