I can do the thing(s) listed to get the achievement (build my first spy center, build Marines on 2 planets etc) but I never get the achievements unlocking?

Seems to me to get achievements you have to launch the game from the Galaxy Client. Even then it seems to forget sometimes. I'm not sure the cause of this. But so far I have gotten like 85% of the achievements by making sure I followed the above. Also seems to work better if you have allow Galaxy overlay turned on - but that might just be a coincidence.

I know from testing when I was getting some of the individual achievements for the races, I would win but not get the achievement notice. Exiting the game, re-launcing from Galaxy Client, load old save position, re-win game and then blame I get notification that the achievement was met. So not sure what is really up with this?

I can not seem to get any of the achievements for defeating the game in all scenarios using race X but that might be cause as I said it like loses the connection occasionally.

I noticed in the log file that it shows what race has won what achievement - I'm going to pull that and figure out which ones I'm missing credit for.

OK I went and made certain that at least for race SAKKRA i had won all victory conditions but the achievement does not unlock - so at least that achievements looks to be not working.

LOG is showing:
DIPLOMATIC_WON_SAKKRA:1
ECONOMIC_WON_SAKKRA:1
EXCELLENCE_WON_SAKKRA:1
CONQUEST_WON_SAKKRA:2
TECHNOLOGICAL_WON_SAKKRA:1

I've started getting achievements now... I whitelisted the MOO exe and everything from the GOG Galaxy client in my firewall.