Blender .STL exports are too small when imported in Sli3er I'm aware that blender units is the default in Blender. And, I think I've changed everything to metric where necessary.

In Scene:
Units is set to Millimeters
Length is set to Metric
Unit scales is set to 1.0 (though I don't fully understand the function of unit scales)

Then, I have (for example) a simple cube with x/y/z of 40mm.
[edit] meant to mention that I also scaled the model back to 1 with CTRL-A - Scale, so that everything is at a scale of 1

I export the file to .STL, but when imported in to Slic3r it always comes in as .04 mm (4/100th mm).

I've imported items from thingiverse, and they import to the correct sizes. So, I'm 99.9% sure this is a blender configuration issue. Anyone know what I'm missing?
By default, 1 Blender unit = 1 mtr, as evidenced by default gravity value in the scene settings.

You could try setting the scene unit to Centimeters (1 unit = 1cm), then scale accordingly. Make sure to enable "Scene Units" in STL export.

For me, leaving the scene at blender units and for STL export enabling "Scene Units" and setting the scale to 10 works fine. For me. For me, this equates to 1 unit = 1cm