Hi Martin,
r39814 broke native vector support because boundaries were not copied, even if they belonged to an area with a cat in the given layer. Fixed in 39975 and 39976. Please make sure that OGR support does not interfere with native vector support;-)
The behaviour of v.clean calling the new Vect_copy_map_lines_field() is a bit unexpected because this is like first extracting all features in a given layer, then cleaning the extracted features. I think the purpose of v.clean is to do topological cleaning, and in a grass vector all features of all layers are topologically linked, thus I would by default always copy all lines of all layers, as in grass6.
I thought about a layer and a where option for v.clean, but not for extracting, all features would be copied, but only selected features would be cleaned, but that means rewriting most cleaning functions...
Best,
Markus