Here is the bug I think I have found - I suspect it is not a feature:
1. I click on "upgrade" to modify a custom ship.
2. After I make changes to the ship I click "save."
3. The interface prompts me with an amount to upgrade existing ships (this only shows up if I have existing ships, to my knowledge)
4. The amount is paid and the interface leaves the screen
5. All of my ship build queues fill with that ship type. Having previously set them to build "nothing" this is a problem. I have to clear every one of them again. As far as I know this does not happen when the upgrade is done outside the build interface.
Forgive me if this has been posted before - I did try to search for anyone having a similar issue and I do not see it in the known issues section. Thanks in advance for your time.
Edit: I am using Windows XP Pro on a dual-processor AMD Athlon MP (not 64) computer with 1 Gb of memory and a GeForce4 Ti4600 256Mb video card. I am also using the latest version of the game and all extras installed, including the special edition items. If you need more information, please ask.