Then: how do you finger these "long" notes? Just the 'B' pinky, or do you depress the 'C' touchpiece as well? Even though the 'B' is supposed to close the 'C' pad as well, this isn't always perfectly the case, especially in freshly repadded clarinets.
Related to this, try fingering B with left hand B plus right hand C. Press a little harder than you usually do when playing. Does this help the B sound better?
Ben is right that it isn't always adjusted very good, but for a freshly repadded clarinet it shouldn't be a problem IF it was adjusted properly. Maybe it wasn't?
I was taught to always finger the long B with left pinky on 'B' and right pinky on 'C' until a) the pads have reached their final seats and b) I was comfortable enough to single-finger the B.
If the adjustment is good, there is no problem playing the B (or E) with any finger or fingers imediately after the pads were replaced. Of course if the keys on a specific clarinet tend to go out of adjustment, in combination with a player who presses especially hard, then it might go out of adjustment sooner than usual. But still the fingering doesn't matter, IME, based on players having this adjustment made to their clarinet, and using all sorts of fingerings for E/B imediately after.
If all the other notes are good, especially if low E and F full and resonant, I don't think you have a leak.
I'll almost put money on the wacked out Selmer register vent.
But what do I know, I'm not a tech.
Some leaks can actually only affect some notes, and low F and E would sound fine in spite of them. I don't really know a specific leak, other than the F/C-E/B adjustment, that would affect only long B, but it's possible.
Re the register vent, this can be the problem. The register vent is compromised and the B can be affected. However I wouldn't necessarily say "the wacked out Selmer register vent", because some Selmer models don't have this problem at all. Maybe it's a specific register compromise that they chose on some models, and on other models they chose a different compromise.
Tammi, something you can try, and if you do I'd be interested in what you find, is play both throat Bb and long B with the second from top (Bb) side trill instead of the register key. For the long B you might need to lean the clarinet on something while trying (no grip). How do these notes sound with these fingerings compare with the normal fingerings?