The same thing happened to me.
I've created a second "race" for RP reasons (Player controlled).
Then all my diplo stance disappeared.
I got it back when I've added Deepspace Tracking Station on one of these new race colony, so they can detect my ships.
This might be applicable to my situation as well, since a fair few empires have been created in this current playthrough. You see, I'm playing with my brother. I am playing humanity, and he is playing an alien empire. We also created 'Space Stalin', who is essentially the spacemaster race, so we don't know where the other started and have a non-player race to jump to when we boot up the game to avoid accidentally looking at one another's empires. There has thus been a fair bit of system generation and race creation.
We swap the database file between each other. So far, this has worked fine. Now (and I'm loathe to say this, as he lurks the forums as well), I am pretty sure that I've discovered him. I am currently following around what I believe to be civilian ships to get an idea of this alien empire, and to map his route back to his homeworld in anticipation of sending a diplomatic vessel to establish contact. Given my run-in with the precursors, my humanity is taking its time establishing contact until we've gathered some idea of these aliens' intentions and workings. Currently, I know him and he doesn't know me. However, he has a similar issue. He has discovered what we believe to be conventional aliens on a planet, and he can't set his attitude to them either, just like I can't set my attitude to either him or the precursors.
If what you said is correct, maybe it should resolve itself once our empires discover each other? Though I don't know whether the issue lies with Space Stalin.
Yes, they are spoilers, but that should have no effect. You should be able to still set them as hostile. I never encountered something similar.
Caesar, maybe try to do a clean install and copy the database to see if it helps? Or try different version of Aurora to see if the problem is version specific?
They are indeed spoilers, and I have in the past, for the same version, been able to set my attitude to them. In the game in which everything worked as intended, there were no player-controlled races beyond the one generated at the very start of the game, so Kiero's suggestion might hold.
I think it isn't due to the installation, but rather something in the database itself, given the fact that we have both installed the game, and we experience the same issue for different sets of empires. Kiero's hypothesis might thus hold. I haven't modded the game or otherwise messed with the database (I don't even know the password to do so), so that can't be it.
For good measure, I'll attach the database file.
I've covered everything that I believe might be relevant, but I'm happy to provide information where I might have missed something of import.