I have tried a setup like yours and the problem seems to be the fact that the screens are not "aligned". Probably because the 17' one is under a little Unity/Nautilus treats it as more space.
I don't know if this is normal or is a bug in either Unity or Nautilus, but to me it seems a normal behavior. To fix it just align both displays as in the following picture:
So just drag the second monitor on "Display" settings until they are somehow aligned. Also note that the disposition of both screens seems to matter, so if you put 27' screen on top of the 17' one the icons that do not fit on the first go to the second one. If that's what you want keep them aligned but with this disposition:
After applying the new setup you need to order the icons again in Nautilus.