Attached is a save game where some Horatio pops only apply a subset of their gene bonuses but others provide full bonuses.

In the save game:

1. Play as light blue (Horatio).
2. Click on "Manage population"
3. Note the happiness bonuses (+2 from Hot (base), +3 from Kalgeros, +1 from Z'vali).
4. Open up the colony Muzis (home planet)
   
5. Hover over the happiness breakdown for Muzis. You'll see an entry listing the happiness bonus from Horatio population. This is correct.
6. Open up the colony Esh.
7. Hover over the happiness breakdown for Esh. Note how I'm only getting +1 happiness per Horatio pop (from Z'vali bonus) but not the +3 (from Kalgeros).
8. This same issue affects the system Columba, but my other systems are calculating happiness correctly.
   

For reference, here is the order of colonization:

1. Muzis
2. Maaz
3. Esh  (affected by issue)
4. Columba  (affected by issue)
   
5. Khras

Here is the order of gene splicing:

1. Kalgeros (+3 happiness)
2. Z'vali (+2 sci, +1 happiness)

I believe both Esh and Columba were outposts at the point when I spliced the Kalgeros, which might be part of how this issue came to be. They were colonies at the point when I spliced the Z'vali whose bonus is correctly applied to those systems. 

HoratioSpliceBug.zip