What i have encountered quite a lot---> Most of the time when you get just ONE string that gives trouble,
1) replace it..Ive seen "dud" strings that will make you want to break your guitar out of frustration, and in the mean time...its the string
2) If it looks as if the saddle is going "beyond" the bridge, tighten the truss-rod a little and re-tune...you'll notice most ( if not all ) of the saddles will then have to be moved forward a little...
3) tighten/loosen the nut at the truss-rod ( just slightly ) and notice any differences...
You get this quite a lot on "new" guitars as they tend to still be "running in"