Check Civ4BuildingInfos.xml. If any building has iConquestProb with a value other than 100 it can potentially cause the bug. If a building shouldn't be captured it has to be registered as such in CvFinalFrontierEvents.py in the onCityAcquired method (I think that's the right method, at least).

(I play the mod regularly myself and I have no problem with buildings cost as is; that's why I'm asking.)
(I've been looking thru the Tutorials and SDK/Python threads, but everybody assumes it known...)
You can open python .py files with notepad or any other text editor.
(I wasn't sure, as I got a pop up question as to whihc program I wanted to use for opening the .py file.)
Check Civ4BuildingInfos.xml. If any building has iConquestProb with a value other than 100 it can potentially cause the bug. If a building shouldn't be captured it has to be registered as such in CvFinalFrontierEvents.py in the onCityAcquired method
Any building that gives a fortification bonus (such as Star Fortress) needs to be in that list as otherwise the bug will occur. It won't happen with worldbuilder, as buildings added in worldbuilder won't be on any planet, and the bug happens when the python encounters a building on a planet that isn't on the master building list, usually because the building on the list was removed in system capture, but civ doesn't know to remove it from the planet, so Final Frontier does this at the same time. If Final Frontier doesn't remove the building from the planet, that's when problems occur.
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Objection, your Honour! (Although I actually have heard of a creator DLing his own stuff and was quite appalled when hearing this rumour. I do it occasionally to see if the DL link works properly - especially after switching DL mirrors or after a complaint - hey, feedback! - about the DL link not working. So it does happen.)
(I can provide pics/suggestions if you need 'em.)
Anyway, after I come back to modding after some troubles.