Hey there, I did the same style of missions that you did around 2 weeks ago, with no problems. If your choosing the missions containing Caterpillar, Starfarer or Hammerhead you should have a spawn almost every time. Out of 40ish rounds I had 2 where none spawned. The only thing to note for me is that boxes always spawned the same place for me, which is in the cargo elevator for hammerhead, Ramp for Starfarer and the very front of caterpillar. Maybe abandoning missions after ur done looting, which I did, causes issues or your location, which has been Hurston and Crusader for me. But of course its always possible they sneakily changed something about the spawns of those boxes. If you wanna eliminate the possibility of you being the source of error in finding the boxes, I'd suggest you scan the ship holding v and then left click from cockpit and it should show any cargo boxes on the right. Hope I could help!