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There is a bug report already.Basically, the problem is that modules researched to a too high of a mark don't show up at all, where instead they should show the highest mark that hull can mount in the "loudout" screen.
Opened your save. My computer wept. Switched to the ST planet and ship icons filled my screen, so I zoomed out. Game told me that it _was_ totally zoomed out. You could seriously walk from one end of the inner grav well to the other without getting your feet cold.