Worked fine for me.

Before unlocking

After

If I launch the "Galactic Civilizations III" program and load the save file "Bug Before Ideology.GC3Crusade" and unlock "Breakthrough" "Enlightenment IV", the bug is not reproducible for me either.

The save file "Bug After Ideology.GC3Crusade" is a save right after the bug has occurred.

Now to reproduce the bug, follow this procedure:
Exit the "Galactic Civilizations III" program.
Launch the "Galactic Civilizations III" program.
Load the save file "Bug After Ideology.GC3Crusade".
Do nothing.
Load the save file "Bug Before Ideology.GC3Crusade".
(Here you can also notice that The The "Bazaar" button is not clickable as explained in this thread.)
Go to the Ideology screen and unlock "Breakthrough" "Enlightenment IV", the bug occurs, the research points are not allocated.
Return to the Ideology screen, "Breakthrough" "Enlightenment IV" has not been validated.

I tried the procedure three times, the first time the bug did not appear, the other two times the bug occurred.
Try performing the procedure several times to see how it goes.

I do not know if this may have an impact, I launch the game with the shortcut created by Steam and select Steam in offline mode.