Did you fully delete all remaining SH3 files and folders after uninstallation? The SH3 uninstaller only removes files that it added, it does not remove any files that other mods added, so if you installed RUb into SH3 then uninstalled SH3, a number of files would have been left behind.
You really need to:
-(Rollback SH3Cmdr if you are using it)
-Disable all mods that you have enabled via JSGME
-Uninstall SH3 via Add/Remove programs
-TOTALLY delete any remaining files and folders under C:\Program Files\UbiSoft\SilentHunterIII (or wherever you installed SH3)
-Reinstall SH3
-Install v1.4b DVD patch appropriate to your region - that is either the EMEA or US patch. Do not install the download version patch.
-Reinstall JSGME
-Reinstall RUb 1.45 into JSGME and enable
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