I'm guessing that the problem is because the max script is written for other versions of max (7 works fine and I believe 8 does) and there'll be some aspect of max 9 that means the normals are flipped. To be honest I'd be glad its something as simple and fixable as that and that the script doesn't balls up the textures or something like that. When I've been doing building collision files its screwed up the vertex painting and I have to spend literally an extra 20 minutes per poly to make it work properly.
One thing to check is that you have version 0.79c which is the latest version of the script.
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