During the sailing run the loot generator only keeps track of a list of which container *types* will be "kept" (i.e. the ones left after container roll-off due to the prioritization scheme). Then at the end, when you port, it calculates the items each person receives for ALL containers that remain at port time. It's POSSIBLE (just a theory) that the process of computing all the loot at once is causing enough lag or timeouts or whatever, that the loot item distribution cannot finish in time, resulting in all/some loot being dropped by the time the loot panel is displayed.
I tried reproducing this issue at one point, it happened frequently in the busy shard, and either never or very infrequently in the quiet ones (been a while, not sure now). So I'm a little surprised to hear it's a significant problem in the quiet shards as well.
If this is the case, a possible fix would be to calculate all the loot items on-the-fly as each container is rolled into the keeper list. This would distribute the processing load throughout the run, and avoid the big spike at port time. It does have the disadvantage that the effort to compute items for the rolled-off containers is a waste, since those items will be tossed. Although if this really a persistent issue in the quiet shards, not sure if this will fix things or not.