Something Wonky Here?

Ok I finally got my printer to Nicely print pla, fixed a few snags figured out optimal temps and such. Now heres my issue. I can print a single object (18650 battery holder) at a time and they come out perfect, using CURA I multiply the object then save the G-code. for some reason everytime I try to print multiples of the same object at one time it gets almost to the top of the print and looks like its skipping a layer, Im noticing gaps in my holder that cause the top to break off, I finally caught it tonight and was able to witness it, it printed one layer fine and then went to the next but was way to high above the print and the filament would lay right, after that layer the next ones are fine. Has anyone run into this problem and did you find a fix, or is this something other than a software issue? Printer is a A600 Ebay printer (Prusa I3 design) with 1.75mm pla, Extruder=230 Hotebed=70. Ive even started slowing the feed rate down to 50% when it gets close to that area and no help