Steam counts the time from the time you click the icon to the time the EXE shuts down. So hours of downloads of updates in sim over the time you’ve owned the title are also accumulated.
Assuming you haven’t been affected by various logbook bugs that plagued many folks over the life of the sim, then your logbook hours should be considered the accurate source.
Either one of 2 things here:
you were affected by one of the aforementioned bugs and lost hours - I’ve lost about 200 hours of time due to said bugs. I should have almost 1300 hours in the sim so far, but my log states I’m at 1100.
bugged achievements. This is quite possible, since it’s been well known (by most of the active community) that achievements have been broken since launch. Most of my achievements outside of logged time I got for random activities that had nothing to do with the achievement I was granted. And there are tons of reports of that.