There is one small bug in the script that prevents it from producing output, and is easily fixed; the next update will include this fix. But the main problem is that the data is just not there, the replay doesn't contain the cities that exist at the start of the scenario, and that means the script can't even tell which civ is which. It'll figure out Russia and Greece because Russia eventually founds Moscow and Greece eventually founds Athens but that's about it.
I will probably be able to get the missing information from the map included with the scenario, but that'll require a bit more work as I haven't decoded anything beyond what is included in manually saved maps yet.
In general, scenarios and mods seem to be a bit of a problem. The replay files don't nearly include all data required to make pretty pictures, and the script does a lot of guessing, but some of those guesses break when mods and scenarios change the game. For example, the Mongol scenario adds a lot of custom city states...