Yes. I typically select and delete all of the clipping masks as soon as I open in illustrator.
The PDF export is an OK workaround, but less layer information is preserved (they stay grouped, but not named, and I don't think that subgroups persist).
Again, I think the issue is related to the complexity of the exported polygon layer. If I zoom in past a threshold, all polygons are properly represented. out beyond that threshold, some polygons become compound shapes with the same color as the larger (more vertices) polygon.