Hey Angelo, sorry for the trouble!
Actually, no! This is intentional, because people with custom builds typically aren't interested in overwriting them with the default Bootstrap. When you build Bootstrap from the Arduino IDE, your build and version are set to the values you're seeing. HQ sees that you have a custom build, and won't show you the red dot or prompt you to update it.
You can "force" the Scout to go back to a nice clean state using the debug page, here: http://hq.pinocc.io/debug and clicking "Upload" while your Scout is plugged in and switched on. We only recommend using that if, as in your case, you've had some trouble and need a clean slate.
If you have any trouble from here on, just let us know.