Andy,
If trying all of the above suggestions still leaves the B string muted, you might try my Sound is Round method. The B string, when muted, is usually being dampened by the lower side braces being too heavy. This depends on the geometry of the braces and top thickness, but is a good place to start.
Pluck the B string and feel the top over those braces. If there is no vibration there, but there is above and below the lower side braces, then here is your problem. Reshape them into parabolas and work them lower with successive restringings, until you can feel vibration over them. There is a picture of a top I braced on the Tapered/Parabolic OM's subject, showing these the way I shape them, which is copied from those on vintage Martins.
The problem can also be caused by the junction of the upper belly brace with the X brace. It should not butt up against the X, but taper down to close to zero height at this point. Again, pluck the B and feel over this place. I wrote about this 10 years ago in "American Lutherie", #47. John Calkin, head honcho under Huss and Dalton, told me has become a believer in this.
The reason the B string gets louder as you go up the neck is that the higher notes are resonating with rings of smaller diameter, and they no longer pass over these side braces. The upper side braces also influence the treble range, but higher notes, being closer to the cross point of the X, and you can do the same test over these braces plucking the high E string.
At least, these braces are easy to reach...
Scott
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, try a different saddle; often, bone will have a soft area near or under a string, muting that one somewhat. Same can happen if your saddle isn't well seated; check that there's no dust or chips a the bottom of the slot, and draw a pencil line down the length of the saddle,on the bottom, and run it a few times over something dead flat to check for high spots or dips. I use a 600 grit diamond sharpening plate for this(the one that StewMac sells for leveling frets.
