Hi, 

shell-process-popd (in lisp/shell.el) is currently unaware of
comint-file-name-prefix. This is inconsistent with the behavior of
shell-process-pushd and shell-process-cd, and hampers proper directory
tracking in tramp remote shells (see
http://lists.gnu.org/archive/html/tramp-devel/2010-11/msg00013.html
). The attached patch should correct this oversight. 

This is my first stab at contributing to emacs so please be patient and
forgiving if I did not do it right or missed something. 

Best regards, Christian.