Sorry for the late reply. I had a couple of heavy work days, then I spent some time playing on, to see if I could detect any patterns to the bug.
Maybe I should first clarify that this happens in space combat screens. No, I don't see any dependence on the type of encounter or any other condition. Whenever I go to pick up the loot after the battle, it usually gives me only the one item. It only behaves properly sporadically, maybe 20-25% of the time.
However, unlike in my first playthrough, where it became a constant issue (and was one reason I decided to start over), this time it seems to go through cycles. It will occur for 3/4 of a day or so—several combats—then behave normally for about an equal length of time. Sometimes it even starts or stops while I'm in the middle of collecting the loot, with no apparent triggering event.
Other than that there's really nothing else I can say. As I mentioned it just started suddenly while I was grinding for the underverse subunits (both times). There are no other conditions or patterns that I can detect.
I'm currently using v.2.41, the Linux version, but the first time around was about 3 versions ago, Again, I have the saves from just before and after it started, if they would help, and if there's some way to get them to you.