Hard to say just going on that : ) but if you can swing a good setup by a good tech person you'll be doing the right thing. If it has never been setup in a few years of season changes it would be a good idea to spring for it.
Checking for intonation at the 12th fret is good to do but it's only a piece of the puzzle. If the action sneaks too high you might be using more pressure on the fret at certain places, which would make it go sharp. And even though the string height may also be high at the octave, you're probably gently touching it down when checking against the tuner. Or if the strings are too low and right up close to the pickup they might be affected by the pickup's magnetism, even though the tuner says the bass is good on the 12th fret.
Could be lots of stuff. More info? : )