I have the same issue with the Yor Planetary Extractor. It takes All Construction bonuses but only gives Social, so it can't be used to boost the Capitals or factory-type buildings. It's fixable with a simple mod though, literally three letters in the xml.
I assume they left the Yor building this way for faction balance, but I think that Plasma Furnace one looks like an oversight. If the devs want to change it, it should be a similarly easy fix to make.
Found it. If you want to make a mod to fix it yourself:
For instructions on modding in general, look at ModdingReadme.txt under Documents / My Games / GC3Crusade / Mods
- Under DLC / DLC7_LostTreasures / Game / DLC7_ImprovementDefs.xml - Copy that file into your mod's Game folder.
- Don't change the original xml in your actual GC3 installation directory!
- Open the copy, and search "PlasmaFurnaceB" and scroll down to Adjacency Bonuses.
- Under the first NeighborBonuses tag, change "Manufacturing" to "MaxManufacturing".
- Delete the entire section for "Military" from its NeighborBonuses to its /Neighborbonuses.
- Save, and run the game with mods enabled. Hope that does it, unless and until there's an official fix.