I've had this experience with the same strings, although 4 string set. I could not understand what had changed. I asked myself:
1. Had I bought the same gauge
2. Had I affected set up/ studs rod
3. Did I stretch the strings enough
4. Had I wound the strings correctly so the pressure was on the nut correctly
Having eliminated these, I simply left the bass alone for a few days. As I thought I had the original string sound so fixed in my head, that I was driving myself mad with disappointment. I played a different bass for a few days, then went back to the newly strung bass. It was better to a point I had to slightly adjust tone, but I think I got there.
I find John carruthers clips are brilliant. Well worth a watch as "in John we trust" I've learnt lots about re stringing and set up from the smooth voiced luthier.
http://youtu.be/-8uBYIwMevA