A few web searches generally point to neck resonance as the main culprit. This can supposedly be changed by adjusting the truss rod tension slightly (though this may simply move the dead spots to another fret), or adding mass to the headstock (If you've got a small metal G-clamp or similar then you could clamp this on to the headstock, or else try taping some heavy coins to the headstock), or damping the length of the strings on the headstock (try a bit of foam wedged underneath the strings).

Changing string gauge will also change the tension on the neck which will affect any resonant frequencies. This will also change the downwards tension on the top of the guitar body and so affect any body resonance frequencies. Without changing strings, you could simply tune up or down by a tone and see if the dead spots either; move up or down accordingly, stay in the same place or disappear altogether.

Changing string type and/or make may also reduce or solve the issue. Not a cheap test with bass strings I know, so I suggest only doing this as a last resort (or maybe with a really cheap Chinese set from eBay).

If you've only played the bass in the same room with the same amp in the same position, then it's possible it may be a room resonance based effect, where either the bass amp or bass itself is at a point in the room where the resonant modes of the room are at a null point and dampening those particular notes. Being a hollow-bodied bass, it's probably fairly susceptible to being affected by the room acoustics. However, these do normally have a big effect on the lower notes, say below 100Hz, and the fundamentals of the notes in question are at 293Hz and 392Hz, where room modes can have some influence, but normally only by a few dB. But if you are only playing in one room and with everything in the same place, it's worth shifting things around or moving to a smaller or larger room (if you can)

So, a few things to try. No guaranteed results but you never know.