Frank, from Bartelin Barrels, was kind enough to offer up some insight. I'm posting this with his permission:
"The biggest thing that makes the change [in velocity] I'm going to say is a combination of two things. Some fouling getting built up into the bore of the barrel (it's very hard to get the carbon build up out and why some shooters consider clean and what they see are two different things) and the throat breaking in.
So carbon build up and the throat breaking in to me are the main reasons. That's my opinion and also feedback I get on test barrels.
Each barrel is going to be an individual. How nice the reamer left the throat when the barrel got chambered will determine how long it takes for the throat to polish and break in. To me in a good barrel this is the only real thing that you break in. If the reamer leaves the throat really rough it's going to take longer to polish and break in."
He also mentioned ammo from lot to lot (if you're shooting factory ammo) and/or each individual's loads are big variables. If one hand loads, maybe there's a change somewhere along the way.
"How the gun/barrel is being cleaned. A big problem is shooters are not always cleaning the gun properly and or often enough or maybe I should say on a regular basis. As an example a shooting a gun in .308win. vs. a .300wm. Yes the same bore size but the .300wm has almost double the case capacity. So with more case capacity you will increase the amount of powder fouling. If you don't keep up with the powder fouling it will for the lack of a better explanation make things to an extent make the barrel tighten up especially in the throat/chamber are and this will drive up pressures etc....Same goes with a .308win. vs. a .243win. basically the same case capacity in regards to powder but by reducing the bore size from .30cal. to 6mm you've in effect have turned the .243win. into a magnum type round."
"Bullet sizes/diameter vary. Possibly from lot to lot and from maker to maker. As bullets are made the bullet dies will wear and as they wear the bullets tend to get fatter."
"I'll give you two personal examples. My 6x47 Lapua even when new and after x amount of rounds thru it.....from a clean barrel the first two rounds will be 30-40fps slower then the rest. I attribute this to the barrel wanting some fouling in the bore and then it settles right down. At 100 yards that little velocity difference is virtually unseen on the target but at a 1000 yards if my wind call is on those first two rounds will be a 9 and 10 out the bottom. So at distance I will not make a elevation correction until a couple/few or so rounds are on the barrel.
The next example is my F Class gun in .284win. From day one that barrel has not changed velocity higher or lower as of yet. Weather it's clean or dirty and I've clocked velocity thru a Oehler Chronograph from the very first round fired. Every once in a while I will run that gun thru the chronograph watching for changes. It hasn't yet and has 400 rounds on it now.
Why the difference between the two guns? Your guess is as good as mine. Keep in mind the different caliber and or bore sizes. I'm shooting different types of powder as well as I'm shooting different bullets thrum not to mention different lots.
I will also say most barrels if they are going to change velocity wise will usually do it in the first approx. 100 rounds. Your going to get some fouling build up and also the throat is going to break in as well. Then usually the barrel will settle down. That's not me just saying that but also data I've received back from ammo makers using ammunition test barrels in controlled conditions.
I also on average I try not to let my guns go more then 100 rounds in between cleanings. Most high power rifle type matches each day you are shooting around 50 to 100 rounds thru the gun. I will clean my gun after each day of shooting. So that is my baseline. My gun has to go at least 100 round in between cleanings and hold accuracy etc....