Yes, they are. I guess the original one is replaced when i choose to use the CE in steam, right? And yes, both aren't working. I copied the Vanilla-Xenonaut-folder from the Steam-folder to another partition, downloaded the 3 CE-zips (xce, settings and balance) from the website and unpacked them in the mods-folder. Then i followed your install-instruction, started the game with the original exe, activated the xce, switched to the xce-folder, started the exe there and activated balance and settings. Then i tried to start the game with the exe in the xce-Folder - error.
Then i tried the vanilla-exe in the main directory, activated the 3 xce-mods (and the xdivision mod) and it started normally. But is the ce-mod working with the original exe or will there be problems during the game? It seems to me the problem is the exe. Has it been changed the last 5 to 7 days? It worked perfectly fine before.