No funds should be going off the money added to your balance whether you're mining or not. Money money is money you've earned and pools don't take that away from miners. From your post, it just seems like you're confusing earning projections with actual earning.
Thanks. The unpaid balance from Eligius keeps doing down, so I'm looking to see what the reason is behind this. Since a block hasn't been found for a while, since before I started mining, I gather that unpaid balance goes down if I no longer mine there.