Those Pesky Civilians are stealing my ship sequence numbers!!! My freighter class is called Africa Queen. I was merrily popping them out from my shipyard (using auto-numbering, e.g. Africa Queen 001, Africa Queen 002, ...), until one day I noticed something weird - I had "forgotten" to build Africa Queen 007; I had just built 008, but there was no 007! I thought it was my fault, so I slotted the next 2 freighters to be 007 and 009. What was really going on was the civies built a freighter, named it Africa Queen 007 (and another one that was 009), and bumped the counter up. (I figured this out a posteriori by peeking in the data base - there's an Africa Queen 007 that's not mine, and it's in the civie fleet, at which point the light bulb went off in my head.)
This wouldn't be a big deal, except the civilian ships are showing up as potential commands in the F4 screen. I realized something was wrong when I finished building "my" 007 and 009 and found their names doubled in the F4 screen, at which point I peaked in the database.
John