What Chrony are you using ? I had similar problems with a .284 Win shooting over a Shooting Chrony Beta Master.
My problem went away when I smashed it to pieces as advised by many others with prior experience, and replaced it with a MagnetoSpeed.
The very slightest change in light (ie cloud,sun, wind causing tiny variations) saw my velocities fluctuate wildly, just like yours.
No such problem since I killed the Shooting Chony !