I am running version 1.99 of Arnor, but this is a problem I've seen in all versions.

When creating a custom race, the button for "Create custom ship style" is greyed out and unaccessible. It is only accessible when creating a custom opponent. In older versions, this was the only way to change the default ships for my custom races, but now saving their styles via the custom opponent screen only changes the defaults for the opponent version of my race. If I select the custom race for myself, the defaults change back to what they were originally.

Custom ship styles will sometimes disappear from the list when using the Shipyard in the main menu.

Extra ship pieces that I save as Favorites will disappear from that race's favorites menu after loading a saved game.

Let me know if you need more information.