MIM Geddy Lee String Alignment

So I recently purchased a MIM Geddy Lee Jazz Bass that I am liking so far.
The "e" and "a" strings are not aligned with the poles on the pickups though.
The g and d strings align correctly centered between the two pole pieces for their respective strings.
The a string is sitting over the inner most pole piece for its string and the e string Is sitting on the inner most edge of the inner most pole piece for its string. I wonder if perhaps the neck should be seated again?

I will attach a pic, although it is tough to hold the camera with no variance side to side and it is dimly lit.

 

Men has only one string groove per saddle, but I have seen some with multiple grooves.
The g and the e strings are NOT equal distances from the edge of the fretboard, although there is adequate distance on either side. Both my MIM Precision and my Squier VM '77 have equidistant spacing on e and g strings and are lined up to their pickup poles much better.
Having said that, I did have to make some serious adjustments to the truss rod on the GED to get it within Fender Spec. And you you likely know, the truss rod nut is at the neck heel, so the neck has bee off a few times already.