I'm also thinking, that the closing the lid (entering and leaving power saving mode) possibly can be a reason.
It is not occurring all the time, but Windows could be having strange behaviors on changing run-time states.
But with other programs (like development software, office stuffs) running, I did not had any trouble with them, so.
Also with processing database scripts running, I was closing the lid and the system was entering the power saving mode - and still a properly running thread after reactivating Windows with opening the lid at home.
Was not trying so far, to debug the threads...
In a previous post I was adding a tiny piece of Windows batch code which is killing the required running executables (of WindowFX) and restarting the service as a small workaround to not have to reboot the machine and brings back the effect quickly.
Yes, you are right, I'm always leaving the machine up and running, because I'm in daily business need of my running desktop environment, which is definitely nicer with WindowFX.