[quote="suncatcher":29x26nnr]Hi Sheldon,
I've had my ABII for several years and gig with it every night. I've been having some odd intonation problems. I've intoned it perfectly when changing strings(open, harmonic, fretted 12th). It is still almost 10cents sharp when fretted on the 3-6th fret on the G & D string. After that and above the 12th fret it is fine. What the....?[/quote:29x26nnr]
Check to see if your frets have flattened out. What happens w/nickle is that the crown gets worn down and shifts the intonation of the neck sharp, on the flattened frets. Unfortunately the nut doesn't shift too.
If your 12th fret still has crown but the areas you're talking about are flat that would be one of the reasons it could be sharp after strobing. I would suggest capo strobing your bass either on the 5th or 7th fret to split the difference.
A fretted instrument is the most imperfect of all the instruments.
When you tune and strobe your bass do you pluck gently and carefully, and then start playing more aggressively live? That'll do it too.

Also check too see if your PU's are a little too close to the string. The magnets will pull the string sharp if too close in the first couple of frets.