I have found this rather specific bug while modding v1.61 of the SDK. I used the function gDLL->getPythonIFace()->callFunction(PYSpellsInterface, "onCastSpell", pyArgs.makeFunctionArgs(), &lResult) and was suprised to find that the game could not find CvSpellsInterface.py (which I had defined in CvDefines.h). After some testing I worked out that this was because I was using my CustomFolders. As soon as I coppied this into a stand alone mod in Program files/firaxis/Civ4/Mods, it started working.
In other words gDLL->getPythonIFace()->callFunction() does not search the CustomAssets Folder.