I'm not sure why it's happening for you; we're looking into a similar launcher issue for some Linux users, which might address your issue too. Please keep an eye on the next couple of SMAPI releases, and let us know for each release whether the issue still happens. In the meantime, please continue to launch SMAPI manually; as long as Steam is running in the background, I think the Steam overlay and achievements should still work. Can you reply with your latest error log attached? You're using an old version of SMAPI; please update to the latest SMAPI 1.4 release. You should update your mods to their latest versions too.