Both Dave and Charlie b are right that barrel length and the chamber and bore differences between barrels are factors in velocity at the muzzle, but there are two other conditions that might create some differences as well.

You didn't mention what Chrono you are using.
Lab Radar and the units the mount on the barrel measure right at the muzzle but my Oehler 35P and most other chronos measure whereever they are set up (and they need to be set up where the shock wave from the muzzle blast won't impact the readings.)
Use your ballistic calculator to see how much 12 to 16 feet makes in velocity compared to muzzle velocity. Your numbers will be slower with a chrono that is mounted away from the muzzle.

Have you taken temperature into account?
I believe that H335 changes more than 1 fps per change of 1 degree F, maybe as much as 1.25 fps.
You need to know what the temperature was the published velocity was measured and the temperature of your shooting condition to see how much difference that would make.
That might be the largest contributor to the difference in measured velocity, especially if the published velocity was measured in the middle of summer. A temperature difference of 60 degrees could drop the velocity by 60 to 100 fps if you are shooting a temperature sensitive powder (if the published velocity reading was measured at 90 degrees in the middle of summer and your measurement was at 30 degrees in the middle of winter)

To illustrate that you need to consider your powder before you go off the deep end in making comparisons of velocities,
Varget has a 0.032 fps change per degree F
H4895 has a 0.064 fps change per degree F.
IMR 4166 Enduron has a 0.16 fps change per degree F.
N140 has a 0.8 fps change per degree F.
IMR 4895 has a 1.24 fps change per degree F.
The first two are 'extreme powders' and N140 and IMR4895 are not.