Well, (at least in my case) the updater popups were the root cause of my freezes; Malwarebytes and for a while Avast (which I got rid of in favor of a less invasive antivirus app) were the usual suspects. When I'd go to the Task Manager after the freeze to kill the FSX:SE app I'd see that the updaters were running (booooo! :( ). So, I turned off the updater notifications and haven't had a freeze since.
I also ran msconfig and did a Clean Boot and turned off all services that weren't necessary, which not only freed up more memory, but when I rebooted in that "cleaner" configuration, also gave my FSX:SE a slight boost in performance/frame rates.
Just a few ideas. :)
Happy Flying!
APUtech