In the reference software defaults to zero fees, except when a transaction fails to meet it's own tests that would qualify it as a free transactions for relay (implying that its peers would also not relay the transaction). In that case, it uses the minimum fees which would satisfy the relay rules— 0.0001 BTC/kb of txn data. The amounts you're showing indicate that you're making rather large transactions!
(search for nMinRelayTxFee in the codebase)
Reducing it further will just result in stuck transactions, since your peers won't relay them.
Thanks!