I have had the notched drive belt hop a tooth on the stepper drive wheel before, but I can't believe it could hop back on the next layer. In addition, the displacement seems too small to match a belt skip.
Have you reviewed the gcode file to confirm the skip isn't there when it is sliced? I know slic3r sometimes does strange stuff that I can't easily explain, but I haven't tried the program you are using. Repetier Host has a nice line by line graphical way to step through the gcode.