The tier-2 luxury Lost-Cities (NP Artifacts) should produce +2 happiness per population. 

Here is before the resource is applied (+59 from 'planet' - not entirely sure where all of that is coming from anyway, I can only accout for about 40 from anomalies):

And here is after: +499!

Lost-Cities (NP) are contributing 440 happiness! It should be producing 88 (2 happiness per pop):

It's actually contributing five times that amount: +2 happiness per pop per planet. I belive the red part is the bug.

Saves attached.

before.sav

after.sav