Jorev: I just completed a game winning all victory conditions in hard mode as Sakkra (default-not customized).
I researched the entire Tech Tree prior to 500 turns.
By my count I should have unlocked multiple achievements but only unlocked one.

I only received "Top of the Class"(win by Excellence Victory for the first time).

I should have also received:

"Sakkra Mastery" ( win all original victory conditions with the Sakkra)
"With Quill and Word" ( win by Diplomatic Victory for the first time)
"Wolf of the Galaxy" ( win by Economic Victory for the first time)
"Transcendental" ( win by Technological Victory for the first time)
"Kill many and you're a Conqueror" ( win by Conquest Victory for the first time)
"This is just the Beginning" ( win by all victory types with any race)
"Reptillians! ( win by Technological Victory with Sakkra)
"Rule of the Many" ( win by Diplomatic Victory with Sakkra)
"Dangerous minds" ( completely research the Tech Tree and win by Conquest)
"Unscathed" ( win by conquest without losing a single colony)

If anyone knows why any of these achievements would have been denied, please advise.

Otherwise it's very frustrating that these are bugged atm.

WhatIsSol: I know they are achievable since I have 100% on the game in GOG Galaxy.

Using non-default (custom) races is the most common issue people have.

Did you launch the game from GOG Galaxy and keep GOG Galaxy running in the background?
Oh, if you still have the saves for something like "Reptillians! ( win by Technological Victory with Sakkra)"

Try this:

Launch GOG Galaxy
Make certain In-game Overlay is turned on for Master of Orion
Launch game from within GOG Galaxy Launcher

Load the save up,
Use timeline to go back in time from just before you won.
Save the game to a new save slot
Load that new save slot.
Win again

See if you get the achievement