The do retract only when crossing borders is the flag which indicates that only crossing perimeter travels will have retracts before them. Choose that mode to speed up print process. Plastic that running from nozzle on travels will be all inside a part, so it will not be visible. If you want to do retract before all travels you should uncheck this flag.
The avoid crossing borders flag is the flag which indicates that border crossing minimization mode in on. It means that if it is possible to travel from one print area to another without crossing borders, that path will be chosen instead of direct path with borders crossing . This mode increases print time, but improves external surface quality.