I've not had a 40 minute gap, but I have had a 5-10min one quite regularly (Athlong XP3200, 1gig RAM, blah blah - i.e. it's a mid-end machine, on a savegame with the maximum galaxy size, inhabitable planets, etc. Not sure if it's down to the sheer amount of stuff saved, or to my HDs being a bit creaky, or even because I have the game on my F: drive and it's using stuff from My Documents (C:) when the 2 drives are on the same IDE cable. Quite odd, though. I also see quite long (~5 mins ish) on the ship editor/constructor screens when a custom design is being loaded.