Nanaimo there are a couple other things that I didn't seem mentioned, did you perhaps use magnum primers with those loads? If you did that could account for the difference between the listed velocity and what the chrono measured. Another thing is to pull the bullets from a couple of your rounds and weigh the powder to confirm that you actually did have 5.5gr of Unique in them.
Assuming you used standard primers and didn't have a problem with your loader tossing to much powder I'll go along with the others and say the problem is with the chronograph.
Let us know what the second round with the chrono results with.