sounds to me like you have a problem with some residual traces of the NYGM-TW mod still present even though you tried to uninstall/roll it back. NYGM-TW messes around the some files equating "renown" with "tonnage" in order to do what it wants to for its tonnage-based system (it uses tonnage rather than renown for various things).
You may want to consider starting over with a completely fresh new re-install of SH3 and of RUB, rather than relying on the Sh3 Commander rollback or even JSGME deactivation (I use both of those programs and they're great, but I have heard that they may leave some traces of old mods behind, especially if you install and uninstall things several times. Kind of a hassle, but might be worth trying.
Good luck and good hunting!
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