How about this last item in the trouble shooting steps :
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People also need to keep their Video Card drivers up to date from the Video Card manufacturer. Such as Geforce owners can go to the NVidia web site and check for latest version of drivers and Radeon card owners can go to the ATI web site for their drivers. Never get drivers from the Windows Update Website as they are known to cause problems when gaming. If you upgrade your drivers and you experience game problems such as crashing, then back step your drivers 1 version at a time until the game works properly. For some video card users, you may have to adjust your desktop color resolution to 16 bit, but only after exhausting the Driver Version methods. Laptops owners will need to check the manufacturer of their laptop for newer video driver versions.
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or this item :
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Make sure you you are using Direct X 9.0b on your system. It is recommended to reinstall Direct X 9.0b on your system as many games will install components that may cause Direct X 9.0b to corrupt. Those not using Direct X 9.0b is urged to update to DirectX 9.0b for Multi-Player in Starfleet Command III as Direct Play components of Direct X 9.0b is not compatible with earlier versions of Direct X and may cause drops in missions, out of sync, or severe lag during game play. This is stated in the Microsoft Direct X FAQ. To update Direct X 9.0b, you can visit the Microsoft Web Site located at
http://www.microsoft.com/windows/directx/default.aspx .
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or these
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When installing Star Trek Starfleet Command III, Do not install DirectX 8.1 or Gamespy Arcade from the game CD, these items will corrupt Direct X 9.0b on your system.
Make Sure that your system is completely up to date from Microsoft Windows Update web site (
http://v4.windowsupdate.microsoft.com/en/default.asp ).
Before Installing the SFC 3 Patch 1.01 Beta 2 Build v531, make sure that you DO NOT install the items below. The items below are designed for an unpatched game streight out of box (v464) and the items below are already included in the v531 patch, which means that installing the below items before or after the v531 patch will cause the game to corrupt when you install the patch.
A) SFC 3 DirectX 9 Fix
B) Nemisis Add-On Package
C) Borg Mini Compaign
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These are all listed in the readme file.
hope that this helps.