i had similar issues with custom 3d models... i read that you load and view the model over model viewer, fine, check the model routers and try it:
Put the model in map editor and go to edit menu --> find object check if it is in the list... if no in list try it,
open your *.ent file with notepad or similar, find the mesh/*.dae path browser and check if is correct, example
<Mesh Filename="static_objects/No_Do/grail_01.DAE">
If incorrect browser, you can edit it manually or move the *.dae file at correct folder...
check textures, materials and folders
If the model is in browser list, select it, focus and check scale, "maybe the object pivot is not centered" and you dont view it over the grid
check too if "map_cache" file in your custom stories/maps and delete it... reload the map editor and try to add the model, save it and open your map file, check the hirearchy object numbers, fileindex and ID orders...
<FileIndex_StaticObjects NumOfFiles="5">
or
<FileIndex_Entities NumOfFiles="8">
now, in object list, check if your model fileindex is correct here
<StaticObject CastShadows="true" Collides="true" FileIndex="4" Group="0" ID="28" Name="road_3" .....
Now, check the ID, if it have a number exaggerated or very far with another objects, changue it manually
If it not resolve the problem i can check your file if you want...
please sorry my bad english :S