If you are using any scenario file other than the default, then a score is not recorded. Even minor changes, such as this, are different from default and so no score!
However, it's not to difficult to add the score manually, if you can be bothered. Look for the file HighScores.cv3 in the conquests directory and add a line:
Your_Name (Civ Number) (Score) (Difficulty Level) (Victory Type) (Won / Loss)
Your name must be one single string, so any spaces must be substituted with underscore (_)
Civ Number starting at 1 for Romans
Dificulty Level starting at 1 for Chieftan
Victory types being:
0 = Domination
1 = Conquest
2 - Cultural
3 = Diplomatic
4 = Space Race
5 = Retired
6 = Rank
Won/Loss being either 1 or 0
Thats what I do to add a score for my modded games.