The problem: font scaling slider in the Controls menu fails to release mouse and keyboard when the preferences screen gets closed by the game itself, resulting in loss of ship's control.

To reproduce: press activate to jump and enter the Options->Controls screen immediately thereafter (during the warp animation). Click on the slider and don't release the mouse until the next sector starts loading and preferences window gets automatically closed. Upon entering the new sector, you'll be unable to control your ship with a mouse and keyboard. Now enter the Options->Controls menu and try moving the mouse over the slider - it's still moving! Mouse has not been released. Click the slider to fix it. ;)

A minor annoyance, if any, but I've just warped like that to Sedina B-8 full of unbots - no fun at all. ;-)