Display issues like this aren't uncommon in OpenStudio. I would generally expect them with more complicated window layouts than this (unless some of the windows are vanishing too), but some glitches aren't too surprising.
You could try loading it into the sketchup plugin instead to see if that works better (though it's typically worse).
Things that tend to cause problems in my experience can be adjacent windows that share edges, especially if you end up with T-junctions etc. (try to avoid those since they can causes OS to mess up the face coordinates) as well glass doors (if I'm having trouble with a wall with doors I might raise the doors 0.01m to get them off the edge). (see eg. link text for discussion of some similar issues)
Ultimately what's important is that the energyplus file itself is correct. In this kind of situation I'd check the .osm file directly in notepad++ to see if the windows and surfaces are correctly attached to each other. When adjusting geometry in OpenStudio surfaces can sometimes get regenerated and break links between them, so windows get orphaned or you end up with multiple copies of surfaces in the same place, with different windows getting linked to different surfaces etc.
If the model itself is fine on inspection and not showing any errors when you import it into OS or try to run it, then display glitches can be ignored (though they are annoying).
While I don't know about the issue with OpenStudio, EP3 can import complete IDF files (geometry, internal loads and HVAC systems) EP3