The save titled "Sophomores 2" is the turn after the third obelisk was built. You can see "3 out of 3" on the victory status screen, and find them on the systems (Phaeton, Wyrix, and Idrus).

I continued the game and researched the other 2 of the 4 available Endless techs, but also got no science victory. The victory status screen says I need 6 (probably because I have an ally) but only 4 are available to research.

The most obvious potential cause would be that I researched a couple of the victory techs before finishing the obelisks; this might have broken a script.

I'm also using a modified Sophons faction, though it would be pretty bizarre for code that already works for any stock faction to break on a custom one.

I did include the custom faction in the zip file too.

Here's the Google Drive link to the zip:

https://drive.google.com/open?id=0B90TwHOrgClRLTBWbWdZdUlkd0U

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Here you go.

Broken victories.zip

Hello :)

I think either this is something we already have fixed on our end or your game didn't refresh alliances counters properly or something like that, because here's what I have when I load your save and check the Victory conditions:

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So try reloading your game and reach the Victory conditions shown in these screenshots? Maybe that'll allow you to get your well-deserved victory :)

Thanks for looking into it. I was already well into a new game, managed to ally again, and just powered on building obelisks until it triggered the victory.