The one thing that occurred to me was that the scripts have a check in them to make sure the quest is not already running before starting the current round. I assume this is so that each bandit gets to run the quest sequence for himself, then the sequence runs again for the next bandit.
If any of the quests don't get stopped properly, I'd imagine that would prevent them from starting again for any bandit, which would explain why the problem gets progressively worse.
I'd like to see someone write down the quest IDs, and when they see a naked bandit check to see if those quests are running or stopped. If they are running (and they should only run for a few seconds upon entering the cell) while the bandits are naked, stop them and see what happens.
That sounds like it could be the reason. I will try to wrap my head around it, but like I said, the scripts interactions are a bit confusing to me so far. But seeing whether the scripts are running or not is a good idea for a start.
Since the fransmenu trick with restoring defaults and saving the changes definitely worked for me (didn't find any calipers since then in places where I found almost exclusively calipers before) I've made a quick fix that may or may not help. It simply sets the three variables that are set by using the Fran menu everytime you load a savegame. May not work well with luck based loot (at least the version that takes five minutes to update) and requires OBSE (due to getgameloaded being used):
http://www.mediafire.com/?y2ozkmyxmzl
I don't claim that this helps in all cases. It is just a quick fix for those who had good results with the FransMenu thing and don't want to bother using the console all the time. Obviously you can't use the in game loot adjustment anymore if you use it since it will always be reset to default values on load.