when you mean netgen 3D in parallel, is the new implementations where the 1D and 2D are done in serial, and the 3D in parallel for each solid of a compound, no?
if thats the case i suspect that the issue is the geometry of the compound, the viscous layer addition does not like the nodes that are on an edge that needs to be moved (here is an example of what I mean Bug SMESH hexahedron + layer generation issue with internal faces of blocks - #5 by NabilG)
regards,