When using the island toolpath I am always left with minor peaks in the work which the clean tool doesn't clean up. I start with a 1/4 inch followed by an 1/8 inch and then finally a engraving tip to clean up. In the areas less than 1/8 inch I am getting sections not milled out.
Have you tried adjusting the 'FILL' parameter of both the rough and finish tools?
You can also press F9 on the keyboard and that will show immediately where any unmachined spots are occuring.
Post a sample of the file if the above doesn't help you.