I’m having the same issue, though it seems to be related to Quick Edit only.
If I add the values on the normal edit screen then update, the values are saved and are retrieved when doing subsequent edits (though in the very clunky custom field boxes below the main post).
If I add values in Quick Edit then update, the values are saved, but when going back into Quick Edit to do subsequent edits, none of the values are retrieved and ALL values have to be filled back in to have ANY of them saved.
I’ve used this plugin very successfully for a year without any problems, and only started seeing the issue when I upgraded to WordPress 3.0 (which is currently 3.0.1) I’m using Version 1.7.8 of CFT and have not changed the format of the template nor changed the permissions on the database.
