I have a similar issue. Maybe it's the same, I believe I have found the reason for it.
My issue:
I'm printing a very small object, each layer takes not even a second (so claims Cura).
For some reason, Cura is adding code that moves the head to the side, extrudes a bit, then moves back extruding some more.
When viewing the GCode with Repetier Host, I can see the extranous head movements. They make no sense model-wise, as they're about 2 CM from the model.
I have looked at the GCode and noticed weird G0 codes - immediately before a new layer.
When I set the minimal layer time to 0, the resulting GCode contains no extra movements.
But when I set it back to 5 seconds, the extra movements/extrusions appear.
Not sure if this is intended, but it almost looks like Cura is expecting there to be a wipe tower?
I can't upload GCode files apparently, so here's snippets of the file, containing one layer each (same STL, same settings, apart from delay):