No...and yes...jPCT's standard scaling behaviour doesn't allow this. The reason for this is, that jPCT doesn't really use a scaling matrix but a virtual scaling matrix with sx=sy=sz=s. The easiest way to explain this quite strange behaviour is: "historical reasons"...
This may not satisfy you and i understand that. But i don't think that i'll break the current implementation to add support for non-uniform scaling.
However, jPCT 0.90 features support for what i've called "VertexController"s. So you may write yourself a VertexController that does the non-uniform scaling for you...should be quite easy to do once you got the concept of the VertexControllers. This is NOT an ideal solution...i know that. Anyway, it's the only way to do it ATM. Maybe i'll think about adding a real non-uniform scaling later if it's really important to you and you can't live with the "Controller-solution".