XTC, welcome at the CCM2 thread.

It was a good idea to attach the screenshot of your CCM2 installation. It seems your installation of CCM2 was done properly, but you have a problem caused by the VirtualStore of Windows.
The Virtual Store of Windows hosts files of your programs, that can overwrite your current files of these programs in the Program Files (x86) folder. After seeing your screenshot, I think your VirtualStore folder holds a copy of your old normal C3C conquests biq that overwrites your new conquests biq in the C3C mainfolder - and that is the reason why you play the old normal C3C epic game even with the new conquests biq, that holds the CCM2 settings.
So you should have a look where the VirtualStore folder is placed in the settings of your pc and delete the C3C conquests biq that is overwriting your new C3C conquests biq.
The normal path to the VirtualStore is: C:\Users\user\AppData\Local\VirtualStore
The names Users and user must be changed to the names you gave those folders in your pc.
The easiest way to find the VirtualStore in my eyes is a Windows search with the word VirtualStore.
You will find a structure similar to that in my screenshot (in your case with the folder 2K games instead the folder FiraxisGames):
Open the Conquest folder and you will see files similar to these ones:
If this folder holds the C3C conquests biq, this biq should be deleted as you have a backup of your original C3C conquests biq in your C3C mainfolder. Of course my folder in the screenshot of the VirtualStore on my pc at present doesn´t host such a biq. The other files outside the new folders in the screenshot in my eyes do no harm, but are hosting current settings of your last game.
In my eyes it is a good idea, to install a desktop shortcut to your VirtualStore (or desktop link - I don´t know the proper English word for that Windows function, in German the term is: Verknüpfung). This not only allows you to clean up very fast nasty old biqs in the VirtualStore (for changed scenario biqs you have to go to the Conquest\Scenarios folder of the VirtualStore), but - at least in Win 10 - the Saves folder you can see in the screenshot above, normally also holds the save files of all your C3C games and it can be necessairy to delete here sometimes a lot of them, when your harddrive comes short in free space.