When was the last time you checked the intonation? How much did you have to adjust the bridge saddles?
they all had to be adjusted the same amount. not a whole lot, but easily 1/2-3/4's of a turn on each. i probably checked them beginning of summer and it was a tad bit off on the E string.
Ok, no biggie I've had basses go completely whack on me, it's normal. Make sure you're using a fresh set of strings if they've been sitting on there for a while.
You should recheck the intonation a day after you change the strings as well guys. I have noticed they go off a little after the initial set up. Not always, but it's a big pain to everyone when you are out of tune in the studio and you announce that you changed the strings and intonation the day before, and you find out it is you that is out! Not all strings are created equal so its worth a check for the next few days.