Hi,
I found this post about the same problem:
http://wp-types.com/forums/topic/checkbox-always-checked/
I'm using checkboxes field, i created 3 options with value 1,2 and 3. Using Cred to edit i noticed all optiosn are checked.
After some testing i got this problem only if my chechboxes field is set to: When unchecked, save 0 to the database
Using: When unchecked, don't save anything to the database, solve the problem.