Netfabb seems to corrupt the models I export from it

Ok, so I am splitting a model too big for me to print into quarters, then going to add screw-on tabs to those quarters so it can be screwed back together. Because of this, the edges need to be completely flat for it to work.

Here is what the unfinished tab I made:

https://www.dropbox.com/s/5k9yrs1rmo...m-Box.stl?dl=0

And here is what it looks like in MeshLab and Google SketchUp. There are some triangles that appear on what should be a flat rectangular surface as pointed out by SketchUp though, but the face is still perfectly flat:

http://i.imgur.com/cLpRoL4.jpg


The printout comes out looking fine too:
http://i.imgur.com/JdSAqDv.jpg
http://i.imgur.com/M0kzPiv.jpg

So then I load it into Netfabb in order to slice off a diagonal area and make the sides more like triangular legs... and then exporting it the triangles I mentioned earlier seem to get exaggerated.

Here is the model:

https://www.dropbox.com/s/tyrwgv3w28...01%29.stl?dl=0

And what it looks like in MeshLab and Google SkethUp. If you zoom in on the MeshLab screenshot, you can notice very fine grooves all along the lines now instead of the surface being flat:

http://i.imgur.com/onsDAUi.jpg

And the resulting printout:

http://i.imgur.com/fYEOaeN.jpg
http://i.imgur.com/6POQBsY.jpg

For some reason when this model is exported from Netfabb, even if I make no modifications at all, it exaggerates the triangles on it's face and makes them uneven, virtually impossible to see unless you zoom in real real close on the 3D model in a viewer. And this in turn causes my printer to go crazy and print an X-shaped series of bumps all over the face of the screw tabs, making the piece completely useless since it needs to be perfectly flat.

Any idea why this is happening? And how I can prevent it?I have tried deleting the extra faces in SketchUp, but it's own Export to STL function appears to add them back in. The extra faces are not a problem originally though as the piece still prints flat until it has been run through Netfabb. I am using Netfabb to slice excess parts of pieces off as well as assemble the entire model together from all the individual components.