Just to ensure I understand. If you start the .exe with a Space Wars connection, it is working correctly, but if you do not, the achievements do not appear?
If this is the case, as stated in the forum thread this is expected. A game that is Greenlit but not fully released will not have access to steam achievements, you can only test the functionality through Space Wars. If this is not correct, please let me know so I can continue testing to see what may be occurring.