Thanks everyone for your suggestions.
I changed the setting on my site model to 'All layers'. That has helped heaps. Thank you Tamsin! With the site model, I was able to find the source data, I think it was invisable due to me turning off the class 'Survey-Levels'. The few plants that float still do so, but I have individually selected them and entered a z value manually. Looks heaps better & would have re-created the site model if I had time, but I have already spent way too much time on this project!!!!
With the plants being invisable when rendered in final quality renderworks - I think this is a issue with the 3D plant image props I used. I tried to render these plants in a blank file and they would only show up in openGL, but not if rendered in Final Quality Renderworks. The plant image props come from the library file 'Aus Plant Image Props 2012'. I'd be interesed to know if anyone thinks these image props are faulty or if it's me & my computer???