God-Emperor
Deity
A few game options have been set to a default setting and hidden form view since they are almost never changed by anybody. They still exist, but you can't change them without editing the XML (well,you didn't use to be able to: see the second fix below).
The main problem with this is an inheritance issue. A game of Civ will inherit the setting from the last time you played regardless of whether or not you used the same mod the last time. Going from one mod to another the settings can have different meanings (and after the first few in the list certainly will unless the two mods are closely related) but it only remembers the settings in the order they are listed. So if you play a mod after playing some other mod you can inherit some pretty random settings that are undesirable. If the game options are not hidden you can see what these are and change them. When a hidden option is changed there is nothing to indicate the situation on the setup screen so you are stuck with unwanted option settings when you start the game. I suspect this is what happened to you.
There are two main fixes for this situation, the first of which works with any mod.
First, if you run a game via "Play Now!" instead of "Custom Game" it should change all the settings to their default values. These new settings should "stick" so they are used the next game you start, so the usual thing is to start a game (usually on a duel sized map just to make it go faster) then immediately exit and start a new game with the desired settings. This does nothing for an existing game.
Second, if you are using C2C v30 the worldbuilder has been expanded and somewhere in there is a new screen where you can change the active game options. Changing some of them may cause problems, but most of that should be fixed by exiting the WB, saving the game (normal save, not worldbuilder save), exiting the game entirely, then loading the new save. A few side effects may linger and changing some of them may make no difference (for example, turning off goody huts may have no effect at all since having it on caused them to be placed when the game started but turning it off does not go though the map and delete them all - unless Platyping and/or the C2C port have implemented this feature and I didn't notice). CHanging the Always Peace option change should work fine as far as I know, although if you also had the "Start as Minor Civs" option set then the part of that which made you start at war with everyone may have been circumvented.
There should be another way around this issue for future games. In the mod's .ini file (Caveman2Cosmos.ini in the mod's folder) there is an option called "ForceGameOptions". If you set that to 1, when you start a new game it should override the saved settings from whatever mod you played the last time (even if it was C2C) and force them to be the default settings from the XML (unless you change them on the Custom Game screen). If you switch between mods you may want to do this. The only disadvantage is that you will have to set every option you want every time you play C2C since it will always start up set to the defaults, it won't remember the options you had set last time which might become irritating if you start a lot of games and always turn on some options.
The main problem with this is an inheritance issue. A game of Civ will inherit the setting from the last time you played regardless of whether or not you used the same mod the last time. Going from one mod to another the settings can have different meanings (and after the first few in the list certainly will unless the two mods are closely related) but it only remembers the settings in the order they are listed. So if you play a mod after playing some other mod you can inherit some pretty random settings that are undesirable. If the game options are not hidden you can see what these are and change them. When a hidden option is changed there is nothing to indicate the situation on the setup screen so you are stuck with unwanted option settings when you start the game. I suspect this is what happened to you.
There are two main fixes for this situation, the first of which works with any mod.
First, if you run a game via "Play Now!" instead of "Custom Game" it should change all the settings to their default values. These new settings should "stick" so they are used the next game you start, so the usual thing is to start a game (usually on a duel sized map just to make it go faster) then immediately exit and start a new game with the desired settings. This does nothing for an existing game.
Second, if you are using C2C v30 the worldbuilder has been expanded and somewhere in there is a new screen where you can change the active game options. Changing some of them may cause problems, but most of that should be fixed by exiting the WB, saving the game (normal save, not worldbuilder save), exiting the game entirely, then loading the new save. A few side effects may linger and changing some of them may make no difference (for example, turning off goody huts may have no effect at all since having it on caused them to be placed when the game started but turning it off does not go though the map and delete them all - unless Platyping and/or the C2C port have implemented this feature and I didn't notice). CHanging the Always Peace option change should work fine as far as I know, although if you also had the "Start as Minor Civs" option set then the part of that which made you start at war with everyone may have been circumvented.
There should be another way around this issue for future games. In the mod's .ini file (Caveman2Cosmos.ini in the mod's folder) there is an option called "ForceGameOptions". If you set that to 1, when you start a new game it should override the saved settings from whatever mod you played the last time (even if it was C2C) and force them to be the default settings from the XML (unless you change them on the Custom Game screen). If you switch between mods you may want to do this. The only disadvantage is that you will have to set every option you want every time you play C2C since it will always start up set to the defaults, it won't remember the options you had set last time which might become irritating if you start a lot of games and always turn on some options.
Nice timing I didn't expect a new version for another 1-2 weeks. 
It looks like almost everything is there. The Pangea mapscript is apparently defective. I was wondering why I sometimes have trouble loading it. And I always use that mapscript too. But Tectonic has a pangea option, so I guess I'll be using that for now on. Thanks! 
