I noticed something similar. When extra permimeter is on, on small objects especially pins that need to fit into a hole (thingiverse thing:23030) they do not fit at all. the holes are printed to small and the pins are printed to big.
When scaling this thing to 35% and printing with a 0.2mm nozzle, the holes in the small gears disappear completely and are filled. when deactivating extra perimeter, it seems fine (at least in pronterface preview).
Maybe this helps in fining the bug.