I have had this happen to me. I'd installed a few mods (no idea which ones - sorry) over a patched version of SH3 and as already described above, all my tonnage was listed as neutral. I uninstalled everything (including the main game - hadn't backed up D'oh!!!) and re installed and now (touch wood) it's all hunky dory.
Sorry I couldn't be more help but at least you know that it's not just you!
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