As I remember, the process for using the milkshape plugins correctly has quite a number of steps that must be followed correctly and are easy to do INcorrectly. Can you post a step-by-step description of how you are doing the import and export of the mesh?
If you're editing the original mesh, the usual mistake I made in the past was to perform actions that would re-order or change the verticies of the mesh. Import and Export options must be set correctly to avoid this.
If making a new mesh around an existing skelteon, the problem was usually moving bones by accident.
First, I assume you're editing a mesh, not creating a new model mesh, correct?
When importing, the "Insert extra triangles to preserve morph targets" should be checked. This seems counter-intuitive since the general idea is to *not* modify the structure of the mesh, but this is indeed supposed to be checked.
When exporting, the "Use existing skeleton' option should be used. Select the original .l3d file from which the file was imported.