When you said you reimported, did you mean you imported v2 layouts, or did you get the working ems layouts?
I downloaded the most recent EMS layouts that WebAssist had available in my account. As I recall these were available with the various other CSS Sculptor 3 files. I don't recall the versioning of the layouts themselves.
But once I used the Preset Manager to remove the EMS layouts that were misbehaving, and reimported this new set of EMS layouts, the layouts worked properly. The layouts once again displayed the font sizing in EMS.