Substance is altering my geometry

I have found that, with a particular set of geo, substance painter is altering the shape of the geometry.

Unfortunately, I can't share screenshots (NDA), but I will describe the issue.

I am working on a mesh comprised of several different pieces. A number of which crash into each other. When visibly comparing my original geo in maya to what gets imported into substance I can visibly see that the positions of various pieces have changed and when I look at the ambient occlusion map that is generated by substance when imported to mari I see that there is more shifting around of geo than is obvious by a naked-eye inspection of the geo itself, as the ambient occlusion does not match the actual geo crash points many places even though it looks correct in substance painter.

Troubleshooting steps I've tried:

- I have generated and exported my ambient occlusion maps multiple times for checking in mari
- I have checked many times over to be sure of which geometry I am using in substance.
- I've exported my geo multiple times and brought it into substance both as an fbx and an obj file. It's doing the same thing in both cases
- I've checked multiple times to be sure that I'm using the same geo in mari
- I've pulled several of my exports, both obj and fbx, back into maya and checked them against the original - they match.
- I've tried freezing and resetting the transforms before export and upscaling to real-world units (as per maya - we are using a 1/100th scale to match houdini). Neither of these makes a difference.
- I've tried this in multiple fresh scenes and instances of substance
- I've tried it on two different computers and get the same results on each
- I've looked over the import and scene settings in substance and haven't found anything that seems like it could account for this behaviour.

Any useful feedback is very much welcome.