"hg pull -u" is the appropriate way to update your local repo with the latest from the Galaxy distribution.   There are various reasons why some of you files may not be updated ( conflicts, changes to you local repo, etc ).  You'll need to look at the hg log for potential problems when you update.  Also, "hg help" will provide a list of the commands you can use with hg, some of which may help you determine problems in your repo if any exist.