Even with that 0.003 balance had been swept out until the last satoshi. The thing on here that you had seen that output of 0.25 bitcoins you should didn't tend to put up another 0.05 balance because its clearly seen that someones do have the access of your wallet. All transactions which haven't done by you do signifies someone do have your seed this is the most possible case why this thing do happen and that's an easy money for that hacker and as suggested above never use that wallet again. Clean your pc or better to reformat it then install electrum then store up seed not on cloud.