Hi Mumbles27 ( Andi )
When you turn off the levels in the files, either the reference files or after they are merged into the master
turn them off using Global Freeze or Global Display ( DWG layers love the freeze option )
MicroStation users tend to display levels off in 1 View using 'View Display' AutoCAD won't recognise levels turned off in one view & on in another. It will recognise levels tunred off Globally ( all views ) or Freeze ( all views ).
Levels can be Frozen or turned off globally using the Level Display dialog or Level manager dialog.
See attached image for the 1st option.