The problem was fixed.
The comments above are asking why ergoemacs-mode reimpliments the command loop. The bug states what the ergoemacs-mode command loop does. It also shows how to turn it off.
As far as low-quality code, I'm unsure what @Mark means by that. However, there are a suite of tests to make sure the functionality is preserved.
I do ...
In step 23 of the startup sequence emacs inserts initial-scratch-message into the *scratch* buffer.
That step is after loading the init file, after running after-init-hook, and before emacs-startup-hook.
Ergoemacs uses its own themes defined with ergoemacs-theme.
The standard theme is defined in library ergoemacs-themes.el.
The value of initial-scratch-...
Ergoemacs binds C-x to kill-region by default. You can free C-x and C-c by evaluating:
(setq ergoemacs-handle-ctl-c-or-ctl-x 'only-C-c-and-C-x)
Alternatively, you could tweak ergoemacs-ctl-c-or-ctl-x-delay. C-c and C-x work like the default Emacs keybindings only if you press another key within the specified delay (which is set to 0.2 seconds).