Mis-Aligned layers .. sometimes (no replies)

I can not reconcile what is going on. If I print a plate with, lets say 8, small parts like an action figure, layers misalign. See pic

So what do you do? Print a 40mm tall calibration cube. And it comes out PERFECT! See pic

Mendel 90 MDF
Ramps 1.4
Printing from computer using Pronterface
Slic3r
Nophead Marlin optimized firmware

Belts tight. Extruder and steppers perfectly calibrated.

Any insights?

- Jim