Based on what you report, I believe Keith is correct... it sounds like a resonance dupe. A little extra mass might correct it or at least move it 'out of the way'. Just to further eliminate geometry problems, take a very close look at the trueness of the fingerboard right there... look for any noticeable groove. Use a credit card and backlight with small flashlight, see if there's any unusual relief there. Believe me, it doesn't take much on a fretless.
On those saddles, that one does look like a replacement... actually, it looks like ebony against the obviously rosewood one next to it. I would think any competent luthier could make suitable replacements for those. Shoot, I'd be willing to try if you sent me a couple to go by. That said, if you have metal (brass?) replacements, I wouldn't hesitate to use them. A black or brown Sharpie pen will keep you in stealth mode.
~Gregory (who freely confesses to be a loothier...)
I haven't had a chance to take a good look at the fingerboard - there was more wear under the A string which doesn't seem to be having much of an effect.
I've been playing it a fair amount with the new strings - it's addictive! Still having some tuning issues but it's partly because I'm playing along with old recordings which may not be at A=440 so I have to try and retune - easy enough if the tune is in E, A, D or G, but not when it's in F or Bb or something like that. It's challenging but fun!
So I don't think there is going to be any time soon that I'm going to take the saddles off - I should have ordered a set when the guy I bought the metal ones from still had them (a couple of years ago I think). It's ok though, I'm going to use them for now and probably won't do anything unless one cracks/breaks.
(Still haven't experimented with the Fat Finger - gotta remember to do that)
Just to keep a record, mostly for myself, I played along with some O'Jays tonight - It's Your Thing, Who's That Lady, and Summer Breeze. A couple of nights ago it was parts of Soft Machine
NDR Jazz Workshop, of course James Brown - Hot Pants, Cold Sweat, Escape-ism - Sister Sledge - We are Family, Chic - Good Times- that's all I can remember for now