Sorry, haven’t looked at the VRF formula in detail, just know in principle how it works. I nominate @AndrewWestberg. 
What I would do: Change the VRF key of the pool. How to Check if your VRF skey is properly registered to the Ledger might help in this. Especially, you have to wait three epochs for the new one to take over. (Others might comment on if this is a bad idea.)
My reason is that it is then not critical anymore if the old VRF key with which you have the problem is known. Makes it easier to get help in what @Terminada suggested, which would also roughly be what I would suggest. (And in the unlikely case that we really find a problem with the formula or code it is easier to say: “Here! Look! Here is the problem!”)
Ideally, we exhaustively check all slots back to the time, where you were still producing blocks.
And we can also plot/check the distribution of the random numbers themselves (the ones that have to go below the “limbo bar” given by your stake proportion).