3D Piece is printed in "negative"

Hi there,

I'm having this problem... I did this 3D model of a case

Attachment 8619

and the first time I printed it, it was pretty good but some holes where not in the correct place. So I did some changes in my original 3D design, like doing the walls of the case more bold and move some of the holes in groups.

After this changes, the printed piece was not correct. After the printer finishes with the base of the case, it's starting to fill it again, like there is another base on the top of the first base:

Attachment 8620

That's why I'm saying that it is printed like in "negative", because it's starting to fill the empty parts and leaving empty the parts that should be solid.

My process to print is the following:

1. Do the 3D design in 123D Design software.
2. Export it from here to a STL file.
3. Open this STL file into Replicator G app.
4. Generate the GCode file (with the settings mentioned below).
5. Build the S3X file (to print it from an SD card).
6. Put the SD card on the printer.
7. Print the piece from SD card.

This was the process that I follow everytime. I also do this for the first time I printed the piece and this was the result (please ignore my notes in blue):

Attachment 8621

And these are my GCode settings:

Attachment 8622

If the model has overlapping or missing edges, the program will try and fill them it automatically. Are you doing a print preview first? you should be able to see this issue before printing and rectify. If using Netfabb is causing the holes to be filled that means the mesh is in bad shape and has many non-manifold sections. Netfabb is good, but it's not perfect.