Thanks for reporting back.
My guess is that it has something to do with the way the original files were created. If you're noticing that the problem is isolated to a group of files all from the same source then the issue is probably with that source. Geometry is difficult for some programs to generate correctly, and bad geometry is notorious for causing problems with the way models are rendered in MatterControl. Essentially, the model files must be pretty close to perfect for MatterControl to accept and display them properly.
If I ever have any trouble getting models to display correctly in MatterControl, I run them through netFabb: https://netfabb.azurewebsites.net/
It's a model repair service (now) owned by Microsoft, and it does a great job of fixing any problems related to the geometry of the model. Once I do that models usually show up fine in MatterControl.
Keep us updated if you come up with anything new.
