Hi Walter,
This is a known (but unfortunate) behavior. IB segregates accounts by asset classes but transactions in all of them are linked to the same "cash" portfolio. We take the cash position reported by IB as truth so non-equity transactions in the same account do affect your algo's available cash.
One Solution is to create multiple linked accounts or sub accounts to segregate the accounting. Run your equity algo in one of them and do any hedging / derivative trades in another. You can still use the "what-if" risk navigator and view reports of the consolidated accounts though. Sorry for the inconvenience but I can't think of a way to fix this without disregarding IBs accounting which would feel very wrong.
David