I've noticed this problem too, but I have not had any trouble with it since I started to rename all the master objects as I make them. Carrara's very fussy about master (objects and shaders). The times I have had this problem there have been two masters with the same name, and, I presume, one gets overwritten. Howsomever, I try to avoid boolean's (though sometimes they're necessary), as they are currently not very good in Carrara, and need quite a bit of cleanup.