It appears to me that your printer is just printing one layer of material over the infill, causing your holes, go to the full settings in Cura under 'Fill', and set that to a higher number like 1mm or 2mm and see what happens. That will add more layers of material over the holes and hide them. Of course, that being said, although I have Cura 14.07, I've never actually used it for an entire print, so I may not be the best authority on the subject!
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