Huh? That sure sounds like a bug. I will look into it when I get time to do so.
For example here when negotiating with the dutch colony:
Wild animals aren't supposed to appear in your diplomatic options.
If you've modified the scenario in WorldBuilder, be sure to keep #47 and #48 as follows:
Those are for wild animals and the church. We should let those players be generated automatically by RAR.Code:BeginPlayer Team=47 LeaderType=NONE CivType=NONE EndPlayer BeginPlayer Team=48 LeaderType=NONE CivType=NONE EndPlayer
I made several changes to the vanilla game: I installed TAC, after that I installed R&R, In your map file RAR Americas Gigantic.ColonizationWBSave I deleted the line Speed=GAMESPEED_TAC_NORMAL, but the entries you mention are unchanged in that file.
And I added
<City>Port Royale</City>
as the french colonies first city in the CIV4CivilizationInfos.xml file and changed swedisch Fort Christina to
<City>Fort Kristina</City>
Edit: Oh, and I added the two files from your 1650 scenario
http://forums.civfanatics.com/showthread.php?t=541535
and did the change to be able to zoom out farther that you mentioned here:
http://forums.civfanatics.com/showpost.php?p=14220812&postcount=974
and the change to more autosaves that Nightingale shared.