It's hard to tell what's going on as long as we can not reproduce the problem (deterministically).

ok apparently ^R doesn't work quite the same in Fundamental mode. this was my clue:

CRM Buffer                 Size Mode             File
.   .e                     2933 Fundamental      /tmp/.e
    .emacs                 2933 Emacs-Lisp       /tmp/.emacs

so, i expect this will help:

(setq-default major-mode 'text-mode)

it does seem evil definitions are active in Fundamental mode, but perhaps undo-tree isn't?