Not sure if this is relevant, as I don't completely understand the question, but I thought I would throw it out there anyway.
If you are having a problem with the fact that jPCT calculates a different center for your object than what you expect it to be, you can use methods setCenter() and setRotationPivot() after calling build() for your object. Also, the setOrigin() method could be used to define a position in world space to begin translations from.
Usually you kind of have to play around with each model you create before it appears the way you want it to in jPCT (the same is true when transfering something from one modeling program to another, so this is certainly not unique to jPCT). A model's scale, rotations, and center are very often not exactly the same as you want them to be, since these things are, after all, relative in nature.