Just to be clear. The variation is 500-800 fps as in the difference between 1500 fps to 2300 fps or 1800 fps to 2300 fps or are your bullets actually clocking at 500 fps and 800 fps?
Neck tension would be my first guess, but primer seating might be the culprit.
What powder and primer are you using? If a hard-to-ignite powder and standard (not magnum) primers, you might get a lot of pressure variation there.
The "high precision scale". Is it electronic or balance beam? Some electronics are sensitive to things like the electronic emanations from flourescent lights or being moved or line voltage fluctuations. The better ones are less sensitive, but still...
I would put a baffle (plywood?) in front of the barrel with a small hole in it about 12" away to catch the muzzle blast and any stray powder granules that might be confusing your sensors. You could move both the Chronograph and the readout unit another few feet away to furthur reduce the chance that muzzle blast is the culprit.
Do you get the same sort of variation with factory ammo in that gun?
Does the powder fill the case pretty well (like 90% of the way to the base of the bullet) or is there a lot of room for the charge to be in different positions? Sometimes a considerable variation in velocity can be produced if the powder is piled up against base of the bullet (far from the primer) or right close to the primer. Though that is unlikely as a source of your puzzle, as the .223 case is not that large.
That's all I can think of off the top of my head.
Good luck, Thanks for asking our advice.