Automatic rule validation will fail to resynchronize a segment if the segment has been modified in any way during the refresh or edit (if a line has been inserted in the segment code, for example, or if the text of a line has been changed). You must re-synchronize these segments manually. Blank lines are OK.
Note, too, that if the code for a segment is duplicated in a program, the autovalidation method will synchronize the rule with the instance of the duplicated code nearest to its previous location, whether or not that instance was originally associated with the rule. The rule will be the same, but the program context may be different from the one you intended. Here, too, you will have to recreate the rule manually.