Have you checked your own ship cash balance when dropping commodities off at base, because if you've set a 3k price on them to buy for. The base will be buying them from you for 3k, or anyone else if not reached full stock limit allowed (base funds going down). But you should notice that because your ship funds would go up after selling them to base. You have to sell to base, then what base pays you - put that cash back in the base bank again. Otherwise the base will never make anything from them, keeps buying for 3k and sells again for same 3k (no profit gets made).
Add to that bases use certain commodities to do repairs and keep it running dropped off, so base ends up losing money if you're not mining or dropping off other commodities "for free" listed for sale at a price, and ones that the base doesn't need itself.
You also say you buy BA that base uses up. Have you checked stock limit on how much is listed on base? Also, have you put a stock limit in place on BA, how much of the stuff can be sold to base? If you've not set a stock limit, you could have somebody selling tons of BA to base none stop, why all your funds are gone. I'd check how much BA is currently listed on base, and if you have it limit capped. That could explain things. People selling BA to base, so cash always going down and base is using BA up. And people buying diamonds for 3k sending that stock limit down also.
Other than that, sounds like you might have a another player who somehow has base access to login and change things. Seems odd base leaking cash and commodities away, never heard that one before. Have you checked base to see if any other accounts are listed apart from your own. Somebody could have got your admin password before and then created another base account using it - one your not aware exist. You should check base to see if any others do, that you didn't add?
