Problem with top layering in Slic3r?

I've got an update to this as well..... although it's more of an guess than an update.

I thickened up the walls on the model, and both netfabb and Repetier stopped complaining that the model was not manifold as soon as it was exported from 3ds max, and the netfabb repair job no longer adds a solid bottom and fills in the trigger area.

So I'm guessing a large part of the problem was 3ds exporting a model with a near-zero thickness surface/wall.

(example of new, thicker file attached.)

..... although it looks like I'm going to have to edit the gcode for this manually. The 1st 5 layers are wrong, but that may have been caused by the 3ds thickening causing areas of the model to swell. I'm looking in to that.

 

Minor update:
Instead of editing the gcode manually, I just went into netfabb and found the part that was sticking up slightly. I did a cut on it, and everything seems to good.

It looks like that one small section increased beyond the borders when I told it to thicken up the model insides.