Windows appear in odd places in Yosemite

Since upgrading to Yosemite when it came out, windows in different apps randomly appear in odd places - eg, not connected to their parents window. Here's the Chrome search bar:

Sometimes it's worse, sometimes it's better, but it's never 100% OK. This happens in multiple apps. Restarting the OS or the app does not help. How can I made windows appear in normal places again on Yosemite?

Might be worth trying to login as another user, either creating a new user, or using the guest account to see if it happens there also, if it does not. It would suggest the issue is with the preferences in your user account, especially if it only happens in some apps, you can look to clear their caches and preferences. However if it continues, I would suggest backup and reinstall the operating system.