upgrade ship broken

I have noticed something like this - the core ships you start the game with, flagship, colonizer, maybe miner too, when you try to design to upgrade them in the shipyard _sometimes_ the modules etc take up less space in the initial version, so when you remove them you can not even immediately add them back in in the existing space.

I kind of never liked that you started with ships you could not actually build anyhow (for instance nobody starts being able to produce a survey module, yet every empire has one on their flagship). I would prefer a check box option to have all races start with no ships in the game.

neal c, you are talking about Twilight, correct?  Can you please send me an e-mail detailing what race you're playing, what ship you're trying to upgrade, and a save game with instructions on how to reproduce this bug? Please make sure to zip the save game or it may block up the mail server.  My e-mail is carielf@stardock.com