I'm using Cura 2.6.
I imported an STL into Cura and it looked fine on the layer preview, layer 1 had the bottom layer visible, the start of some supports, and there was a skirt around it. After I scaled it to 200%, there was no longer anything but the skirt and supports on layer 1, the actual bottom didn't start until layer 2, and the skirt had changed and was now overlapping the bottom of the model.
I created this model by taking a model of Thingiverse and using a plane cut in Meshmixer to cut it in half, so the mesh should be perfect flat at this point. I also uploaded the model to Netfabb and got the same result when I scaled it up to 200.
I thought about playing with the Z axis and bringing the model slightly into the bed, but I cut this model in half so I could print the two halves separately and glue them together, I don't want them to be uneven when I go to put them together.
The other half is fine when I scale it up, layer 1 remains the bottom of the print.