Interestingly, I don't see that option in Preferences at all. Also using version 2.0.16 on Windows 10 (although 14393)

@lxalln That's odd. Can you see anything between Use Nylas Mail as default mail client and Show icon in menu bar / system tray if you check Developer Tools?

Html:

<section>
    <div class="item">
        <input type="checkbox" id="default-client" value="on">
        <label for="default-client">Use Nylas Mail as default mail client</label>
    </div>
    <!-- react-empty: 40489 -->
    <div class="item">
        <input type="checkbox" id="core.workspace.systemTray" value="on">
        <label for="core.workspace.systemTray">Show icon in menu bar / system tray</label>
    </div>
    ...
</section>

React is hiding the option, which leads me to:

Looks like SystemStartService is returning false from checkAvailability(), which appears to be checking for read access to _launcherPath() which is looking for a folder in %LOCALAPPDATA% called nylas. The folder in %LOCALAPPDATA% is actually called NylasMail, which would be why the option isn't showing for me.

I didn't install until 2.0.15, so perhaps you installed a previous version, and have the nylas folder, thus enabling the option, which creates the wrong shortcut.

I can confirm that running that Update.exe does not actually launch the app, just updates the SquirrelSetup.log file with a line that says 2017-04-20 18:02:52> Program: Starting Squirrel Updater: but doesn't actually do anything else.

Looks like it should be calling the nylas.exe file that's in that same folder. Which does launch the app, and does check for updates whilst it does it.

@davidbgeek Opened a PR (#3443) which should fix this.