I've been having this trouble for a little while. Whenever I open a new file in spacemacs, it always opens in fundamental mode. I'm on a clean install of spacemacs on windows 10 if that matters.
To see what the content of auto-mode-alist was, I opened the scratch buffer, started an inferior emacs lisp, typed the variable name, and pressed enter. I saw a lot of output, the first of which was the association of *.el files with emacs-lisp-mode. So I tried opening a new .el file, but I still got fundamental mode. I then set auto-mode-alist to contain just the association of *.el files with emacs-lisp-mode. I opened another new file, but I got the same result.
So here is a question: is there a way to disable the auto mode choosing of emacs? Is there a setting that could possible interfere with it that I might have accidentally somehow set (but I'm on a clean spacemacs, so I don't know how it would happen)?
Note, non-spacemacs emacs works fine.
I should also note that when I open a file with windows line endings, I see lovely ^M characters at the end of all the lines. Without spacemacs, emacs picks up on the line endings and acts appropriately by hiding them.