I'd rebuild your MD first without overviews to see if there's any issues with displaying those rasters normally. Be aware of the MD layer properties to only display x rasters otherwise show a wireframe. Have a look at the MD attribute table and see if Min Max PS give anything away (I've experience of these randomly being different for some rasters). Z Order shouldn't be an issue however. If everything looks OK, define and generate overviews with your own settings. Start small scale and iteratively go larger scale overviews to test.
