Sorry for the slow response, has been an extremely busy week. My guess is that something went wrong with the Rationalism tenet. Had you adopted it? What civ were you playing?
No problem, I saw the GP glitch in 1692, loaded the 1680 savegame and have not seen any problem again (in 1788 now).
Here is some information and savegame downloads.
civ: El Cid, Spain
Tenets: Animism,Honour,Pluralism,Enlightenment,Scripture,Sacrifice
Civics (before Golden Age):Theocracy,Slavery,Warrior Code, Retribution,Regulated Trade,Citizenship
Civics (starting Golden Age):Confederation,Subsistence,Warrior Code,Liberty,Regulated Trade,Citizenship
Settings: Prince, Archipelago, Epic
I just finished the Museo Del Prado in Cordoba by sacrificing a slave (1682), and get 7 extra GP in Valencia. I only noticed 7 rounds later because an unexpected Great Scientist appeared in Valencia (which had 63 specialists by then).
The savegames can be downloaded here (please don't judge my lack of strategy):
http://herrdebby.netsec.be/civ4/