Your problem must be one of procedure.

When making the second bar, start from scratch, don't try to copy from the first bar. The second bar should originally have the 4 default menu items on it.

Lets assume you did that, when you go to save the menubar, it must get a different name than the first menubar, it could defaulting to the same name, and writing over the first one.

Assuming also you are not using FP or Dreamweaver.