Hey guys,
We have a fix in for this and are in the process of testing it. We should have a release within the next week or so. Thanks for your patience, and sorry for the inconveniences to your projects/workflows.

In the meantime, there is a workaround (I posted this above):
The latest versions of Substance Painter (6.2.0, 6.2.1) seem to be having problems with the dcc-plugin side of it and UE4. I looked a bit into it, it seems to work as expected if you use Substance Painter 6.1.3 and below.