To me looking at those numbers I should not have had such good groups
Yes and no. A 100 yard group with a poor velocity statistic is a possibility for some situations and only adds to the suspense of what you will find.
My guess is like the others... I think your chrono numbers are suspect.
The point of my post is to say you can not tell what the velocity stats are by looking at a 100 yard group size, good or bad.
With your situation, using a Lilja bbl in 22-250, it is possible to have poor velocity stats and good 100 yard groups. A good rig can stay inside half MOA at 100 yards shooting a huge ES just depending on the harmonics of the bbl and gun. When the bbl section is relatively heavy, a good rig can print small with a very wide range of velocity at 100 yards.
In a situation like this, the math on a typical 22-250 trajectory that assumes the bbl is infinitely rigid would allow for less than 0.3" change at 100 yards just due to velocity. When you consider that no rig is infinitely rigid and that luck plays a role in small group samples, it is completely possible to print small groups at 100 with a good rig using poor velocity stats. That said, I do really still agree it is more likely that your situation is due to the chronograph issues. ETA: That same ES becomes a full minute of vertical difference at 600 yards, or roughly 6" of vertical just due to velocity and much easier to interpret.
I would borrow a LabRadar and shoot at least 10 rounds and see what comes. If the velocity numbers look very different from your optical chrono, I would try a little distance to make sure the muzzle blast pressure wave isn't getting to the sensor before the bullet passes the second sensor. That sort of issue can cause lots of noise in an optical chrono. If you can also shoot the string before lighting conditions can change, it also helps avoid the errors with sky screens.
If you cannot get over a tie breaking chronograph, the obvious way to see if those velocity numbers are really that bad is to put it on paper past 300 yards. The vertical due to the speeds will leverage themselves and make it much easier to interpret the results.