I generally find that Alembics are slow to respond to neck tweaks via the truss rods. Between the laminations and the 1/4 ebony fingerboard, they're STIFF. On one hand it's a bit aggravating as it really does take a day or two for the eventual 'stopping point' to be reached. On the other hadn, there's nothing worse than a Flexible Flyer neck, you know, one of those necks you can just bear down at the nut end of the fingerboard and you can see it / hear it flex. These can turn into a real handful if you are sensitive to changes in feel.
I find on my two fives (a '92 and an '06) that it really takes 24-48 hours for it to finish moving. Can NOT imagine waiting on one with ebony lams !
I could see the relief could be just flat enough with the bridge low enough on the high side to where when it's played, as it vibrates it's just ever-so-barely grazing a fret to damp it in a not very audible fashion. On the other hand, you'd think it would also catch the D, maybe even the A out as well. Or owing to Alembic's adjustable nut (2-piece high- and low-side on a Five), it could be the same thing happening from the other end. But if you follow the steps David outlined above, I'd think you could trouble-shoot that pretty quickly.
IF I was betting, I'd think p/u height and/or the occasional brand new, quick-and-the-dead ('but I just bought these!') string.
Personally, I'm no fan of XLite strings, because every one of these 'can't hear my G or C' posts I see seem to always involve XLite strings.
I'd check my p/u clearances with a ruler. I'd start off getting them even/parallel to the strings (that is, both across and front to back) as a baseline, listening to them carefully through the amp (where I'd run flat if I could to not fool myself into hearing something that may not be there). If they're light or heavy on one side or the other, adjust accordingly, and I'm sure this will go away.
Don't even get me started on room anomalies . . . Standing Waves Hate Me.
J o e y