Yes, I looked at the pictures. We tried to reproduce the issue with the model and settings you linked to but were unable to.
In its current implementation, Expand Thin Walls is really meant more for touching up small areas within a print that would otherwise not render properly without the setting enabled. It's not intended to be used to expand an entire perimeter like the box you're trying to print. The walls are 0.5mm, which is exactly the nozzle diameter, and this makes operations difficult for the slicer. Increasing the walls even to 0.51 would be much easier for MatterSlice to work with. I will make a note about the issue you're having with the functionality of this setting, but I don't expect any quick changes to the way it works so you'll probably want to modify the model instead.