Interesting to say the least, I have not ever encountered this, and as far as I know rent does not have a negative impact like that.
IMO I think the storage/rent thing is sorta stupid, I wish we could choose for example a building/cave/etc as a place to call our sg/vg's home and based on what it is then rent should be scaled accordingly.
For example a cave would have a very low rent cost, while a large building in Talos would have a high rent.
Sorry to get off topic, I searched everywhere I knew and found nothing. My best advice is to file a /bug and see what the response is.GL 
I have an SG base, and I am the only active member.
I check the registrar to see how much closer/further away I am from the top 100. (Hey, it's just something I do.)
So, I noticed that today I had less than yesterday. As far as I know, the only thing that's supposed to impact banked prestige is if someone leaves and that loss puts you below 15 members, or if you pay the base rent. I did not pay it.
So, why would the SG registrar show me as having almost 11k less than I did the day before. I ran a posi, a synapse and even a few hero tips in SG mode. So, I'd say I'm really missing almost 100 to 150k prestige.
Any ideas? Does waiting until two weeks after the rent is due cost some sort of interest penalty?
"Most people that have no idea what they are doing have no idea that they don't know what they are doing." - John Cleese
@Ukase