I just recently started having the same issue. Turning cloud saves off didn't help. What did help however was turning off steam overlay for Factorio specifically. I think it's somehow related to some of the newer versions of nvidia drivers, because just months ago I didn't have this problem. What's ...

Maybe make the main menu invisible if there's no input for x seconds and make it reappear on any kb/m input?
Glad to hear that it's getting fixed. This is the first time I've ever seen myself something that would be considered a bug.