Man, the theories on this issue are wild!
I believe that's because there is more then one bug listed here. For instance, the hyperdrive bug (which I haven't seen) seems to be something completely different. My games have had hyperdrive, but the bug I'm talking about has been present from start to finish anyway.
As regards the bug, where 1) ships created in the shipyard disappear (after creation and then reopening the shipyard) and can no longer be marked obsolete or deleted, and 2) that ship design can still be built on planets even though the ship no longer appears in the shipyard, and 3) that the ship just saved in the shipyard (ie. the shipyard has not been closed and reopened yet) display the wrong ship or wrong components, that problem has been remedied in all of my testing by simply making sure you use a name that has not been used before.
If you are not saving ships to the hard drive (by disabling that option), then you likely won't have ever seen this problem, but I have not verified that. However, turning it off after you have previously created ships, which have therefore been previously saved to disk, still leaves you with the problem. You can not name your ships the same as what was used previously, as they are still present somewhere, even if you delete them from the ship folder. This is what leads me to believe the names might be saved in some list in the registry or something (combined with someone who said they uninstalled and it didn't fix it).
This problem is also linked, at least in all of my testing, to the hosed up graphics in the shipyard. For instance, I create a ship, name it something that has been used, and save it. The new image, after saving the design, will not match the actual design I just created. Again, deleting everything in the ship folder, will not remedy this. And of course, upon closing the shipyard and opening it back up, the design no longer shows at all.
So, somewhere along the lines, if the ship already exists from a previous game, it must be improperly indexing the new design and you get an incorrect ship displaying after creation in the shipyard. And upon future views in the shipyard, it just can not pull it up at all and is likely just returning null in the search routine. This implies that the routine to list all ships is done differently in the shipyard where you can't see them, wherein the main galaxy view you can still build them. Of course, my theories on the coding side here are all speculation, without seeing any code. But everything else outside of why the code is doing it, appears to be standing the test in all of my games.
I hope I have sufficiently detailed what I am seeing, so that SD can look into it and fix it. This is a consistent issue, not random. It is persistent from start to end, in every game I do.
taltamir, how do you set it to not save ship designs?
Just go into your options. It's on the first tab, rather then one of the others like audio.