If you want to use the ESI i would ensure first that your numbering scheme follows the system given in the ESI interface.
So one part master in Windchill should be one part in SAP -- if your numbering doesn't follow this rule i'd consider building my own interface because this would break the internal logic of the interface.
By the way -- My personal thought is that this JMS thing makes the whole interface much more complicated than necessary. If you have some trouble it's really hard to find out the location where the problems come from because the code is very splitted up.