Your bass has a dead spot - right where they always are. That dead spot steals the fundamental of a note played there fast. If you put rounds, on your bass, the overtones hang around for a while so it isn't as "dead". With flats, the string itself kills the overtones, the neck steals the fundamental, and...it's a much more obvious dead spot.
The cure is often to add (or subtract) mass from your headstock - your bass neck is what we Acoustical Physicists call a mass loaded bar - changing the mass loading will change the frequency at which the neck vibrates, and move the antinode to a place where you're not playing that note - kinda difficult to explain completely. If you take half the tuners off your bass (the E and A ones, leave the G string and its tuner on), and the dead spot is alleviated, then a set of lighter tuners (Hipshot Ultralites) is the real cure.