While I agree that the paintball has more forward (read "along the flight path") momentum at 300 fps, its lateral momentum is very small. Given that the lateral forces are proportional to velocity squared, higher velocities will result in stronger sideways "kicks" to the paintball each time a vortex is shed.
Additionally, the 300 fps constant velocity results in a greater shedding frequency (though quite possibly an equal shedding spacing) than lesser velocities. So if you use a decelerating model, you end up with around the same number of vortes sheddings, each of which is smaller in magnitude than a shedding at 300 fps.
Then again, you have more time between sheddings, so those weaker "kicks" act over a longer period...
I think this could go either way, or could well end up coming out exactly equal in terms of paintball shot distribution. <--- and if that ain't a catch-all sentence, I don't know what is.
As for the 2 meters versus 0.2 millimeters... you're missing the units on the graphs. Matlab just loves to put powers of ten in the corners of plots. For example, the histogram has at the bottom right corner of the plot "x10^-4", meaning all the x-axis numbers should be divided by 10000. So you end up with 2/10000 meters, or 0.2 millimeters.
I plan to try to increase the complexity of the flight model to incorporate deceleration, but it truly was a nasty piece of code to work with during my first attempt. I'm thinking it may take a couple of weeks of off-and-on work to hammer the thing out properly. Working on my home computer leaves much to be desired, too... for some reason the software I'm using wants to poll all my hard drives each time I move between coding and execution windows... bizarre. Eventually I'll upgrade to something with a bit more sanity to it.
On a side note, I've also begun to take a look at what effects a slight bias of the shedding orientation would have on the paintball's flight characteristics by changing from a uniform orientation distribution to something more gaussian in nature. The effects can be quite profound (and sometimes bordering on the absurd) for certain gaussian standard deviation parameters. If a (relatively) slowly spinning paintball can induce such a shedding bias perpendicular to its axis of rotation, then this could well explain the deviations we're seeing.
Someday I'm gonna write all this up in a dissertation and get my Doctorate.