Ok, that sounds like an issue with the way lpub handles parts (for Bill Of Materials and such). I think we may need a tutorial for this because I suspect you need to move the synthesis bits into separate files to have lpub treat them as parts. These separate files could also be combined into one MPD file. I don't honestly know if MLCad will do that for you, or if you need a separate utility if you don't want to do it in a text editor.
Do you have an ldr file you could share for testing?
Do you have an ldr file you could share for testing?