Yeh, you should be getting fairly close gauss readings from your magnet, magnet length can effect the charge they hold, but with alnico rods, once the length goes past x2 diameter they won't get any stronger.
So if you've passed your mags through your neo's a couple of times, they should be holding a full charge, unless the rod was previously charged with the opposite polarity, you can't change the polarity of an alnico rod and bring up to full charge with Neo's, for that you need a proper magnet charger.
Another possibility is that you've got an A2 rod mixed in with your A5's
As for taking measurements, you'll probably find that you get the strongest reading from the top edge of the magnet, rather than in the centre.
Hope that's of some help.