Just incase it's not fixed, I'm running a testnet node with 0.15.1
estimatefee 6 returns 0.00000999 while the relayFee is actually 0.00001000 -- note that this doesn't affect estimateSmartFee which is returning a more sane 0.00001008.
Anyway, I realize estimatefee is deprecated but it's still probably worth chucking in a MAX(x, relayFee) there until it's removed [assuming it hasn't since been fixed]