Mule is not compatible with Nemacs. Sometimes .emacs made for Nemacs causes trouble when used for Mule.
To share the same .emacs, you have to divide it into two parts; one for Mule and the other for Nemacs:
(if (boundp 'MULE) (functions for Mule)) (if (boundp 'NEMACS) (functions for Nemacs))
There is a sample of a sharable .emacs file in the texinfo manual of Mule. It may help you.
Note that some of the byte compiled files are NOT sharable. Concerning about this point, Enami Tsugutomo <email@example.com> writes:
You should prepare two different files for Mule and Nemacs if you want to byte compile those files.
As Mule and Nemacs adopt different internal representations of kanji characters, you must re-byte compile if the files include kanji characters.