I've noticed this sometimes. Earlier, I opened a fresh map in the MP editor and placed one ammo crate. Exported / saved to MP missions. Previewed the mission & the one crate. Went back into the editor, added more crates, saved / exported to mp missions, hit preview and the lone crate is still there. None of the newly placed objects are there.

I've deleted the old .pbo, in hopes it will atleast create a new updated pbo upon save. Still only one crate appears (from the first save), yet I've clearly placed several objects in the editor.