Second layer of ASA print 'runs'
I've now worked out the reason for the plastic 'running' on the second layer. It is because of the way that I prepared the G-Code file, using the option in  Slic3r which lets you alter the layer height for certain layers in the print. The problem with this appears to be that there are other settings which are not altered at the same time for the thicker layers. So the first half of the file ends up printed using the settings that work for a 0.05 mm layer height, but with the layer height set to 0.2 mm.

I have prepared a new file by rendering two G-Code files, one using the Prusa settings for a 0.2 mm layer height, and the other using a 0.05 mm layer height. I then merged these manually by looking for the layer change at 2.8 mm in both files and appending the end of the 0.05 mm file to the start of the 0.2 mm file. (I found the layer changes by using Slic3r's custom G-Code option, and adding custom comments into the G-Code which included the layer number and height on every layer change). Then I inserted an M600 'Change filament' instruction at a height of 3.05 mm, where the writing begins.

When I print this file, the problem with the plastic running together on the second layer disappears.