I'm having this same issue. I'm currently trying to use cura and come away from simplify 3D. The simplify file prints fine but cura messes up towards the end of the print.
It's not the filament as the simplify file is good.
It's not the printer as again the simplify file is good.
It's something in cura. Both cura and simplify are using same speeds, temps, retracts ect.
Any ideas?