This site is being deprecated.
Please see the official X‑Plane Support page for help.
Do you know what FPS you're getting? It sounds like it may be pretty low if mouse click response time is so long. Go to Settings > Data Input & Output & check the last box on line 0 to see the FPS onscreen in the cockpit.
If low FPS is the issue, you'll need to try adjusting the rendering settings. Large monitors, high resolution, extremely detailed add ons and more can negatively affect FPS.
While the question is a bit different, I think the response on this issue might be helpful in figuring out if your issue comes from a GPU or CPU bottleneck.
This site is no longer being actively maintained.