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Well there could be a couple different things going on. OS 10.12 is pretty new and has not been tested extensively, so it may have changes that negatively affect X-Plane. Typically we do not recommend upgrading to the latest OS very quickly.
The second thing is that you made a huge jump in terms of updating. 10.8 is four operating system versions ago. Each OS update tends to get more powerful and include more default features. It's possible your computer is overwhelmed by the new OS and all its features. (I will not update my iPad 2, for example, to iOS 9 or even 10 because I have read that it makes the iPad 2 too slow to use because of how much system resources the OS needs.)
This site is no longer being actively maintained.