I am having an issue where I will have a post with custom meta data and I save a post and it holds the value. Then on update or resave the value won't hold. I am not getting empty I am getting a "1" in the field.
To add I found this post http://wordpress.org/support/topic/custom-fields-wont-add-correctly-theme-problem?replies=3 and I removed all blank lines from function.php and that didn't work.