All right, I think we got to the root of all troubles...at least we hope....
We have been working with several 3D models not built by us. We are just providing texturing/lighting. Everything just worked fine until we tried to open the MXS in Maxwell Studio and generate a pack and go to send to the rendering farm. We just could not save or pack and go the files. We spent some time this week and went through all components and try to eliminate components one at the time to see if anything in particular caused the issue. This is what we learned: We found in the models a few elements that had some vertices not connected, these elements were just single polys with different faces ID# and multimaterials applied to them. Basically:
Problematic vertices in a poly with different faces ID#s and use of multimaterials = Pack and go DID NOT work
We then tried the following:
1) Leave the not connected vertices as is and apply a single material to the poly = Pack&go OK
2) Leave the not connected vertices as is, detach the faces of all different materials (so it was not a single poly anymore) and use the original multimaterial = Pack&go OK
3) Remove the vertices that were problematic and leave all the rest as it was = Pack&go OK
To conclude: the issue that we had was due to a combination of inheriting a model with components set up as single poly that had extra vertices and try to use multimaterial targeting different faces ID#s.
The problem is that it would be a huge job to go around and double check all elements of these models and when you have team sharing models on big projects, I can see that possibly happening again. We have a sort of a script that check on extra vertices and removes them but I try not use it on big scenes because sometimes it messes up stuff and you don't really see it at the moment. Works OK for smaller scenes, where you can keep a close eye to results.
My question here is: Is there any way to have an error message that point to the element that is causing the issue? That would help to quickly look at those problematic components. Or, are we better off to just not use multimaterials, considering that with the single material the files just seemed to pack&go OK...
We also found the cause of the problems for the weird rendering artifacts: some of the components had a "double face", looks like the modeler created the poly then detached a face but then cap it again, leaving the extra face there. When we were rendering we were getting very weird results because the materials were sort of blending and show up every time in a slightly different way. Once we cleaned those faces everything went back to normal...