Yes.
I had vibration with mine as well. I used some black rubber sealant on the lid to seal it and the vibration and noise has since ceased (noise quieted a bit). I also put some foam around the box (to seal the fenderwell gap and under box to help with vibration) with some window a/c foam I got a home depot for like $5.
With my JBA EVOL exhaust I rarely hear my intake now

. The only time I've hear it over my exhaust is when I'm in the mountains (10-11k feet or higher) and with the engine working soooo much harder with the thin air I can hear the intake hummm at about 4k rpm's and up.
I have a pre-production kit on my truck and the hole for the tube/filter in the box is not as large as on the kits they sell (Long story short I had to cut the hole out.....I cut it just large enough to force the filter through the hole in the box). You may want to put some rubber/foam there as well to help out with noise if sealing th elid dosen't do anything.
Overall I think the S&B CAI isn't one of the quieter kits out there. If you can't live with the noise I've heard the Tru-flo kits are like stock sounding and the K&N's aren't that loud either. Most of the others I've heard (or read about on the forums) seem to have some noise associated with them.